@article {pmid41506449,
year = {2026},
author = {Zhang, S and Li, Q and Peng, Y and Huo, J and Ran, T and Zhang, X and Wang, R and Jiao, J and Jiang, A and Luo, G and Zhang, Z and Qiu, Q and Li, Z and Mao, S and Yu, Z and Tan, Z and Dong, X and Wang, M},
title = {Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants.},
journal = {Journal of advanced research},
volume = {88},
number = {},
pages = {31-44},
doi = {10.1016/j.jare.2026.01.013},
pmid = {41506449},
issn = {2090-1224},
mesh = {Animals ; *Ruminants/virology ; *Gastrointestinal Tract/virology ; *Virome/genetics ; Metagenome ; *Viruses/genetics/classification ; *Gastrointestinal Microbiome/genetics ; },
abstract = {INTRODUCTION: Viruses are abundant biological entities within the gastrointestinal tract (GIT) of ruminants. Current understanding is extensive for bacterial and archaeal communities, but limited for viral communities.

OBJECTIVES: The study aimed to investigate viral diversity, virus-host interactions and ecological functions of viruses across GIT regions and ruminant species.

METHODS: We collected 373 short-read and long-read metagenomes from 10 GIT regions of seven ruminant species, combining Illumina, PacBio HiFi, and Nanopore sequencing. Viral contigs were identified using sequence homology, viral hallmark gene and machine learning, and employed to uncover community assembly of spatial heterogeneity by analyzing virus-host linkage, lifestyle, and auxiliary metabolic genes (AMGs).

RESULTS: We constructed a Ruminant Gastrointestinal Virome Catalog (RGVC) comprising 43,981 vOTUs, revealing that viral communities were remarkably diverse and mainly driven by the GIT regions rather than by the ruminant species. Virus-host linkage analysis identified 4603 putative prokaryotic hosts across 34 classes for 5954 host-linked viruses, along with robust correlation (R[2] = 0.91) observed between abundances of prokaryotic hosts and host-linked viruses across GIT regions. The lysogenic lifestyle was a dominant feature, with integrases being the predominant lysogenic-specific genes. We identified 864 high-confidence AMGs in lysogenic viruses that are annotated as key genes for polysaccharide degradation, glycolysis, and the Wood-Ljungdahl pathway, indicating a putative role for the viruses in supporting these host metabolic functions. The metabolic features of host-linked viruses were further verified by genomic context of selected AMGs of GH10, GPI and FHS with target function.

CONCLUSION: These findings suggest that the GIT viral communities exhibit spatial heterogeneity with distinct virus-host interactions, and offer new perspectives on maintenance of complex ecological and nutritional functions in ruminant GIT.},
}

Animals
*Ruminants/virology
*Gastrointestinal Tract/virology
*Virome/genetics
Metagenome
*Viruses/genetics/classification
*Gastrointestinal Microbiome/genetics

@article {pmid41539598,
year = {2026},
author = {Wei, S and Li, W and Ran, S and Zhang, J and Zhang, Z and Yang, Z and Tian, F and Chen, L and Hu, P and Yuan, J and Lin, H},
title = {Multi-organ metabolic dysregulation and cecal microbiota alterations following black carbon exposure.},
journal = {Journal of advanced research},
volume = {88},
number = {},
pages = {285-295},
doi = {10.1016/j.jare.2026.01.027},
pmid = {41539598},
issn = {2090-1224},
mesh = {Animals ; *Cecum/microbiology/drug effects/metabolism ; Male ; Mice ; Humans ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects ; Metabolome/drug effects ; Metabolomics/methods ; Liver/metabolism/drug effects ; Microbiota ; Multiomics ; *Carbon ; },
abstract = {BACKGROUND: Black carbon (BC) has been linked to adverse health outcomes, yet underlying mechanisms remain unclear. Integrating metabolomic and metagenomic data across tissues may clarify BC-induced biological pathways.

METHODS: We performed human epidemiology and mice experimental approaches. We included 248,288 participants with annual BC exposure estimates and plasma metabolomic profiles. Elastic net regression identified BC-associated metabolites. Male C57BL/6J mice were exposed to filtered air or BC (1 mg/m[3], 1 h/day, 5 days/week, 12 weeks). Multi-tissue metabolomics and cecal contents microbiota sequencing were conducted, with histology and gene expression measurements.

RESULTS: In humans, long-term BC exposure significantly altered plasma metabolites, notably increasing saturated fatty acids (β = 0.048), while decreasing docosahexaenoic acid (β = -0.002). Amino acid metabolism was broadly disrupted, involving elevated valine (β = 0.011) and reduced glutamine (β = -0.006). In mice, metabolomic profiling showed organ-specific shifts, including increased glutathione and cortisol in the liver (2.88-fold and 2.06-fold), increased PC(16:0/18:1(9Z)) in the heart (3.22-fold), elevated anandamide and arachidonic acid in the kidney (2.35-fold and 1.48-fold), and decreased multiple fatty acids and lysophospholipids across organs. Cecal microbiota exhibited reduced alpha-diversity (Shannon: 3.67 vs. 4.50, P < 0.05) and taxonomic shifts, including an increased abundance of g_Akkermansia and decrease in g_Bacteroides. Multi-omics integration revealed significant microbiota-metabolome correlations in the cecum and plasma (Mantel r = 0.276, P = 0.012). Histological examination confirmed organ injuries, notably lung inflammation, cardiac edema, and neuronal condensation. Gene expression analysis showed increased Il-6 in the lung (5.35-fold, P = 0.047), increased Mb in the heart (5.18-fold, P = 0.010), and increased Igfbp7 in the kidney (3.03-fold, P = 0.001), while Tjp1 expression in cecum was reduced (0.42-fold, P = 0.004).

CONCLUSIONS: Our findings suggest that BC exposure may alter systemic metabolism and gut microbiota, potentially contributing to tissue injury and inflammation. The gut-organ axis could be a target for mitigating BC-related health effects.},
}

Animals
*Cecum/microbiology/drug effects/metabolism
Male
Mice
Humans
Mice, Inbred C57BL
*Gastrointestinal Microbiome/drug effects
Metabolome/drug effects
Metabolomics/methods
Liver/metabolism/drug effects
Microbiota
Multiomics
*Carbon

@article {pmid41539600,
year = {2026},
author = {Li, W and Guo, H and Wang, Q and Peng, D and Wang, Y and Lu, Z},
title = {Phocaeicola vulgatus promote growth rate via tryptophan metabolism pathway mediated gut sIgA production in Taihe Silky fowl.},
journal = {Journal of advanced research},
volume = {88},
number = {},
pages = {77-89},
doi = {10.1016/j.jare.2026.01.022},
pmid = {41539600},
issn = {2090-1224},
mesh = {Animals ; *Tryptophan/metabolism ; *Chickens/growth & development/microbiology/metabolism ; *Immunoglobulin A, Secretory/metabolism ; *Gastrointestinal Microbiome ; Cecum/microbiology/metabolism ; Probiotics ; Metagenome ; },
abstract = {INTRODUCTION: Taihe Silky Fowl (TSF) has a long growth cycle and slow growth rate, how to effectively improve the growth rate of TSF has become the primary concern for breeders. Currently, extensive research has established the gut microbiota's role in modulating growth rate of commercial chicken breeds, while the specific microbial mechanisms influencing TSF growth rate remain poorly understood.

OBJECTIVES: Therefore, this study aimed to identify growth rate-associated key microbial species in TSF through multi-omics approaches, experimentally validate their growth-promoting roles via controlled interventions, and elucidate the species-metabolite-host interaction mechanisms.

METHODS: Cecal metagenome and metabolome was used to search for differential key microbiota and metabolites of TSF with different growth rate, the whole genome of key microbiota was used to identify the relationship between microbiota and metabolites, and gavage key microbiota to TSF was used to demonstrate the effectiveness of probiotics and preliminarily explore their mechanisms of action.

RESULTS: Cecal metagenome analysis demonstrated a significant enrichment of Phocaeicola vulgatus (P. vulgatus) in high-growth-rate fowls, Erysipelotrichaceae bacterium was significantly enriched in low-growth-rate fowls. The differential metabolites between the two groups were significantly enriched in tryptophan metabolism pathway. Subsequently, gene analysis revealed that P. vulgatus encoded tryptophan biosynthesis genes. In feeding experiment, oral gavage P. vulgatus improved the TSF final body weight, average growth rate and average daily gain, increased cecal P. vulgatus abundance, enriched the metabolites in tryptophan metabolism pathway both in the cecum and serum, and upregulated cecal tissue gene expression in the 'intestinal immune network for IgA production' pathway resulting in the higher secretory IgA (sIgA) concentrations in cecal tissue and luminal content than the control group.

CONCLUSION: P. vulgatus promoted the growth rate of TSF by optimizing the cecal microbiota, elevating cecal tryptophan metabolites and stimulating sIgA production via sIgA gene upregulation in cecal tissues, thereby enhancing host immune modulation. These findings elucidated the microbiota-metabolite-host axis governing TSF growth regulation, providing both mechanistic insights and practical applications for probiotic-based strategies to enhance growth performance and gut health in this valuable poultry breed.},
}

Animals
*Tryptophan/metabolism
*Chickens/growth & development/microbiology/metabolism
*Immunoglobulin A, Secretory/metabolism
*Gastrointestinal Microbiome
Cecum/microbiology/metabolism
Probiotics
Metagenome

@article {pmid42155010,
year = {2026},
author = {Kim, JS and Loe, A and Ma, SF and Ranjan, P and Lipinski, JH and Mikhail, SG and Gurczynski, SJ and Zhou, X and Huffnagle, GB and Downward, JE and Metcalf, JD and Falkowski, N and Stringer, KA and Dickson, RP and Huang, Y and Moore, BB and Martinez, FJ and Murray, S and Noth, I and O'Dwyer, DN},
title = {Gut microbiota associate with disease severity and survival in idiopathic pulmonary fibrosis.},
journal = {American journal of respiratory and critical care medicine},
volume = {212},
number = {10},
pages = {2455-2466},
doi = {10.1093/ajrccm/aamag249},
pmid = {42155010},
issn = {1535-4970},
support = {R01 HL162659/HL/NHLBI NIH HHS/United States ; UO1HL128964//NIH/NHLBI/ ; R01HL162659//IPF Foundation, and Veracyte Inc/ ; //NHLBI/ ; K23HL150301//Drews Sarcoidosis Research Fund/ ; R01HL176659//Drews Sarcoidosis Research Fund/ ; UH3 HL145266//Drews Sarcoidosis Research Fund/ ; R01HL130796//Drews Sarcoidosis Research Fund/ ; R01HL153028//Drews Sarcoidosis Research Fund/ ; R35HL176572//Drews Sarcoidosis Research Fund/ ; R35GM16312//Drews Sarcoidosis Research Fund/ ; //NIGMS/ ; },
mesh = {Humans ; *Idiopathic Pulmonary Fibrosis/mortality/microbiology/drug therapy/physiopathology ; Female ; Male ; *Gastrointestinal Microbiome ; Severity of Illness Index ; Aged ; Middle Aged ; Pyridones/therapeutic use ; },
abstract = {RATIONALE: Gut microbiota modify immunity. Dysregulated immunity plays a key role in the pathogenesis of idiopathic pulmonary fibrosis (IPF). However, the role of gut microbiota in IPF pathogenesis is unknown.

OBJECTIVES: Determine associations between gut microbiota, disease severity, and lung transplant-free survival in IPF.

METHODS: Gut microbiota from patients enrolled in the CleanUP-IPF trial were characterized using fecal swab samples (n = 411). CleanUP-IPF investigated the clinical efficacy of long-term antimicrobials in IPF. 16S ribosomal RNA gene amplicon sequencing and shotgun metagenomic sequencing were performed to comprehensively profile gut microbial communities. Associations between baseline microbiota with disease severity, transplant-free survival, and treatment heterogeneity were analyzed using principal component analysis, multivariate generalized linear models, additive models, and Cox regression models.

MEASUREMENTS AND MAIN RESULTS: Gut microbiota composition varied significantly with sex, age, and proton pump inhibitor use. Gut microbial diversity and community composition were significantly associated with impaired gas exchange (percent predicted diffusing capacity of lung for carbon monoxide). Several genera including the Lachnospiraceae unclassified genus were associated with improved transplant-free survival (hazard ratio [HR] = 0.34; 95% CI, 0.14-0.87; P = .02) in patients not assigned to antimicrobial treatment. Patients with a higher abundance of the Lachnospiraceae unclassified genus exposed to long-term cotrimoxazole had worse survival (HR = 6.09; 95% CI, 1.36-27.27; P = .02). Survival in pirfenidone-treated patients was significantly associated with a higher abundance of the gut Lachnospiraceae unclassified genus.

CONCLUSIONS: In exploratory post hoc analysis, gut microbiota correlated with disease severity, associated with treatment heterogeneity and transplant-free survival in patients with IPF.},
}

Humans
*Idiopathic Pulmonary Fibrosis/mortality/microbiology/drug therapy/physiopathology
Female
Male
*Gastrointestinal Microbiome
Severity of Illness Index
Aged
Middle Aged
Pyridones/therapeutic use

@article {pmid42242497,
year = {2026},
author = {Han, J and Lisco, A and Che, Y and Anderson, MV and Laidlaw, E and Kim, CS and Hou, P and Conlan, S and Proctor, DM and Lee-Lin, S and Amirkhani, A and Holmes, CJ and Suh, GS and Brownell, I and , and Segre, JA and Sereti, I and Kong, HH},
title = {Expansion of pathogens and restoration of human skin microbiome in CD4 T-cell lymphopenia.},
journal = {The Journal of investigative dermatology},
volume = {146},
number = {10},
pages = {2840-2849.e7},
pmid = {42242497},
issn = {1523-1747},
support = {Z99 AR999999/ImNIH/Intramural NIH HHS/United States ; ZIA AR041218/ImNIH/Intramural NIH HHS/United States ; ZIA AR041219/ImNIH/Intramural NIH HHS/United States ; ZIA AR041220/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Humans ; *Skin Microbiome/immunology ; *HIV Infections/immunology/drug therapy/microbiology/complications ; *Skin/microbiology/immunology ; Female ; Male ; Adult ; CD4-Positive T-Lymphocytes/immunology ; *Lymphopenia/immunology/microbiology/drug therapy ; Middle Aged ; *T-Lymphocytopenia, Idiopathic CD4-Positive/immunology/microbiology/drug therapy ; Human Papillomavirus Viruses/isolation & purification/immunology ; Longitudinal Studies ; *Microbiota/immunology ; },
abstract = {The microbiome and host immune system maintain a dynamic homeostatic equilibrium at the skin interface. Prior studies have shown that the skin microbiome is profoundly altered in immunodeficient conditions. Patients with idiopathic CD4 lymphopenia, a rare clinical syndrome with an obscure cause, and people living with HIV are 2 etiologically distinct groups of individuals with CD4 T-cell lymphopenia. We conducted shotgun metagenomic sequencing, metagenome assembly, and read-based mapping to examine the multi-kingdom taxonomic diversity of skin microbiomes in patients with idiopathic CD4 lymphopenia and people living with HIV who were followed longitudinally before and after initiation of antiretroviral therapy. Compared with healthy individuals, the skin microbiomes of patients with idiopathic CD4 lymphopenia and antiretroviral therapy-naïve people living with HIV showed greater inter-individual variation and higher relative abundances of eukaryotic viruses. Both patient groups carried pathogenic microbes, including high-oncogenic-risk human papillomaviruses and dermatophytes such as Trichophyton rubrum, which were rarely seen in healthy controls. In people living with HIV, high-oncogenic-risk human papillomaviruses persisted after 2 months of antiretroviral therapy but were mostly cleared after 14 months. The loss of peripheral blood CD4 T-cells was associated with shifts in the skin microbiome and a relative expansion of pathogenic microbes. Investigating microbiome dynamics during immunodeficiency and subsequent immune reconstitution provides additional insights into host-microbial interactions.},
}

Humans
*Skin Microbiome/immunology
*HIV Infections/immunology/drug therapy/microbiology/complications
*Skin/microbiology/immunology
Female
Male
Adult
CD4-Positive T-Lymphocytes/immunology
*Lymphopenia/immunology/microbiology/drug therapy
Middle Aged
*T-Lymphocytopenia, Idiopathic CD4-Positive/immunology/microbiology/drug therapy
Human Papillomavirus Viruses/isolation & purification/immunology
Longitudinal Studies
*Microbiota/immunology

@article {pmid42406122,
year = {2026},
author = {Joseph, S and Abraham, LS and Premachandran, K and Samrot, AV and Thirugnanasambandam, R and Ragavendhar, K and Alodaini, HA and Moubayed, NM and Hatamleh, AA and Mani, RR and Chang, SW and Ravindran, B},
title = {Unravelling Extremophilic Microbiome Diversity and Functional Dynamics in Hypersaline Environment.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42406122},
issn = {1432-184X},
support = {REIG-FPS-2025/038//UCSI University/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Metagenome ; Salinity ; *Archaea/classification/genetics/isolation & purification/metabolism ; Biodiversity ; *Extremophiles/genetics/classification/isolation & purification ; India ; Phylogeny ; *Seawater/microbiology/chemistry ; },
abstract = {Solar salt pans are extreme hypersaline environments that represent functionally specialised microbial communities mediating essential biogeochemical transformation. Vedaranyam, a coastal region of the Bay of Bengal containing artificially constructed solar salterns for salt production. There is limited information available on the metagenome diversity and functional profiling of this saltpan, which prompted us to investigate it. Here, we report the first whole metagenome sequencing to explore the dynamics of the functional structure of microbial communities in saltpan during the preharvest and postharvest phases of salt production. Methanobacteriota and Pseudomonadota dominated both phases at the phylum level, while Halobacteria comprised the most abundant class (53.2% preharvest; 48% postharvest). A notable bloom of Dactylococcopsis salina was observed during postharvest (4.28% to 12.67%) and flock doubling of Cyanobacterota relative abundance (5.5% to 10.6%), reflecting photosynthetic primary production following salt removal. Conversely, during postharvest phase sulfur oxidising Guyparkeria halophila reduced 23 fold, while the DMSP accumulating osmolyte producer Salinibaculum marinum dominated preharvest (6.98%). However, functional classification of the metagenome revealed active participation of the microbial community across five major biogeochemical cycles. Encompassing carbon fixation by cyanobacteria and diverse haloarchaea, nitrogen cycling through diazotrophy and denitrification, a cryptic preharvest sulfur cycle coupling sulfate reduction and sulphide oxidation, phase shifted DMSP catabolism, and light driven bacteriorhodopsin through archaeal energy conservation. Metagenomic assembly yielded ten metagenomic assembled genomes (MAGs), revealing the taxonomic diversity and metabolic potential of the dominant halophilic community across biogeochemical cycles. These results provide critical insights into the ecological succession from an anaerobic, chemolithotrophy-rich preharvest microbial community to an aerobic, photosynthetically driven postharvest assemblage, advancing our understanding of microbial biogeochemistry in managed hypersaline ecosystems.},
}

*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification/metabolism
Metagenome
Salinity
*Archaea/classification/genetics/isolation & purification/metabolism
Biodiversity
*Extremophiles/genetics/classification/isolation & purification
India
Phylogeny
*Seawater/microbiology/chemistry

@article {pmid42554630,
year = {2026},
author = {Tandon, A and Bais, AK and Shrinet, J and Tripathi, V and Gupta, D},
title = {Effect of alcohol and smoking on methamphetamine users' oral microbiome and metabolome.},
journal = {The American journal of drug and alcohol abuse},
volume = {52},
number = {4},
pages = {442-454},
doi = {10.1080/00952990.2026.2697752},
pmid = {42554630},
issn = {1097-9891},
mesh = {Humans ; *Microbiota/drug effects ; Female ; *Methamphetamine ; *Metabolome/drug effects ; *Mouth/microbiology ; Male ; *Alcohol Drinking/metabolism ; Adult ; *Amphetamine-Related Disorders/microbiology/metabolism ; Metabolomics ; *Tobacco Smoking/metabolism ; },
abstract = {Background: The oral microbiome comprises the microbial communities inhabiting the oral cavity, whereas the oral metabolome reflects the small molecules generated by host and microbial metabolic activity. These systems may provide insight into substance-related physiological disruption, including altered inflammation, immune signaling, and host - microbial interactions. Although the individual effects of methamphetamine, alcohol, and smoking have been explored, their combined impact on these systems remains largely unexplored.Objectives: To investigate the metabolic and microbiome alterations associated with chronic methamphetamine use in individuals with alcohol and tobacco use.Methods: High-throughput metabolomic and microbiome datasets from methamphetamine users (Males:168, Females: 50), stratified by self-reported tobacco smoking and alcohol use, were analyzed using integrative bioinformatics approaches, including multivariate and pathway enrichment analyses, to identify dysregulated metabolic pathways and microbial alterations across defined subgroups.Results: The study revealed significant upregulation in metabolites like prostaglandin E2 (log-2-fold-change: 2.63, Cohen's D: |~0.881|, p-val: 7.1 × 10[-10]) and glutamylisoleucine (log-2-fold-change: 1.42, Cohen's D: |~0.88|, p-val: 2.5 × 10[-2]). Microbes such as Bacteroides (log-2-fold-change: -4.91, Cohen's D: |~1.95|, p-val: 1.3 × 10[-4]) and Brachymonas (log-2-fold-change: -2.47, Cohen's D: |~1.09|, p-val: 5.8 × 10[-3]) were significantly downregulated. This suggests that long-term concurrent methamphetamine use, alcohol consumption, and smoking are associated with alterations in microbial and metabolic pathways related to oxidative stress, glutathione metabolism, and neuroactive signaling.Conclusions: The oral microbiome and metabolomic profiles may serve as accessible indicators of substance-related biological disruption. They may also help identify clinically relevant targets for monitoring risk, guiding personalized interventions, and developing informed strategies to support recovery.},
}

Humans
*Microbiota/drug effects
Female
*Methamphetamine
*Metabolome/drug effects
*Mouth/microbiology
Male
*Alcohol Drinking/metabolism
Adult
*Amphetamine-Related Disorders/microbiology/metabolism
Metabolomics
*Tobacco Smoking/metabolism

@article {pmid42647084,
year = {2026},
author = {Díaz-Díaz, LM and Estremera-Rodriguez, L and Rojas-Correa, M and Quintana, MDC and Madziar, C and Hickey, DC and Vargas Robles, D and Méndez, Y and Santiago, A and Bermudez, D and Olendzki, B and Torres, EA and Maldonado-Contreras, A},
title = {Diet quality, gut microbiome, and inflammatory signatures in Puerto Rican adults with Crohn disease: a multidimensional analysis.},
journal = {Inflammatory bowel diseases},
volume = {32},
number = {10},
pages = {1993-2003},
doi = {10.1093/ibd/izag161},
pmid = {42647084},
issn = {1536-4844},
support = {//Leona M. and Harry B. Helmsley Charitable Trust/ ; },
mesh = {Humans ; Female ; Male ; *Crohn Disease/microbiology ; Adult ; Puerto Rico/epidemiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; *Diet/standards ; Middle Aged ; Feces/chemistry/microbiology ; *Inflammation ; Biomarkers/analysis ; Young Adult ; C-Reactive Protein/analysis ; },
abstract = {BACKGROUND AND AIMS: Diet is increasingly recognized as a modifiable factor influencing gut microbiome and outcomes in Crohn disease (CD), yet data in underrepresented populations remain limited. We evaluated diet quality, dietary patterns, gut microbiome composition, inflammatory markers, and patient-reported outcomes in adults with CD from Puerto Rico.

METHODS: We conducted a cross-sectional analysis of 60 adults with CD enrolled prior to dietary intervention in a parent study. Dietary intake was assessed using 24-hour recalls and evaluated using the Healthy Eating Index-2015 (HEI-2015), Alternative Healthy Eating Index-2010 (AHEI-2010), and exploratory dietary pattern analysis. The gut microbiome was assessed by shotgun metagenomic sequencing. Clinical outcomes included fecal calprotectin, C-reactive protein (CRP), a 96-cytokine panel, short Crohn Disease Activity Index (sCDAI), and short Inflammatory Bowel Disease Questionnaire (sIBDQ). Associations were evaluated using unadjusted and adjusted models with false discovery rate (FDR) correction.

RESULTS: Overall diet quality was poor and characterized by low intake of fruits, vegetables, whole grains, and fiber, alongside high intake of saturated fat, added sugars, and animal-derived protein. Four dietary patterns were identified: vegetable-rich, dairy-rich, fruit-rich, and coffee/sweetener-rich. Participants adhering to the fruit-rich pattern exhibited the highest diet quality scores. Higher HEI-2015 scores were associated with greater gut microbial diversity and differences in overall microbiome composition. Participants with greater adherence to the vegetable-rich pattern showed modest increases in microbial diversity. Exploratory analyses suggested that higher fruit intake and adherence to a fruit-rich dietary pattern were associated with lower fecal calprotectin and CRP levels, whereas adherence to a vegetable-rich pattern was associated with better health-related quality of life (HRQoL) and adherence to a coffee/sweetener-rich pattern was associated with a worse symptom burden. However, no associations between dietary metrics and inflammatory markers, cytokines, or clinical outcomes remained significant after FDR correction. Most participants were in clinical remission despite substantial impairment in HRQoL.

CONCLUSIONS: Adults with CD in Puerto Rico exhibited poor diet quality that was associated with gut microbial diversity and exploratory differences in clinical outcomes. While these findings support the influence of diet on the microbiome and clinical outcomes, larger longitudinal studies are needed to determine whether dietary improvements can influence disease outcomes this underrepresented population.},
}

Humans
Female
Male
*Crohn Disease/microbiology
Adult
Puerto Rico/epidemiology
Cross-Sectional Studies
*Gastrointestinal Microbiome
*Diet/standards
Middle Aged
Feces/chemistry/microbiology
*Inflammation
Biomarkers/analysis
Young Adult
C-Reactive Protein/analysis

@article {pmid42806510,
year = {2026},
author = {Singh, S and Sharma, VK and Shrivastav, D and Kushwaha, JM and Mishra, MK and Beg, MMA},
title = {From Rhizosphere to Resistance: Microbe-Plant Interactions in Eco-Smart Biocontrol.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70398},
pmid = {42806510},
issn = {2045-8827},
mesh = {*Rhizosphere ; *Plant Diseases/prevention & control/microbiology ; Pest Control, Biological/methods ; Soil Microbiology ; Plant Roots/microbiology ; *Biological Control Agents ; Microbiota ; Multiomics ; Crops, Agricultural/microbiology ; Fungi ; *Plants/microbiology ; },
abstract = {The increasing limitations of chemical pesticides such as environmental pollution, pathogen resistance, and threats to human and ecosystem health have increased the demand for sustainable, biologically based crop protection methods. Eco-smart biocontrol has emerged as a game-changing paradigm that uses beneficial microorganisms associated with plants to suppress phytopathogens, boost plant immunity, and make agroecosystems more resilient over time. Moving beyond traditional single-strain biocontrol, eco-smart biocontrol integrates multi-omics discovery, artificial intelligence-assisted predictive microbiome design, and dynamic rhizosphere ecology. This review brings together ecological, molecular, and technological dimensions of eco-smart biocontrol, focusing on the rhizosphere as a dynamic hotspot for plant-microbe interactions. We investigate rhizosphere microbiome assembly and demonstrate the preferential recruitment of beneficial bacteria, fungi, actinomycetes, and mycorrhizal symbionts by plant root exudates. Moreover, the review highlights the impact of innovations in multi-omics techniques (metagenomics, transcriptomics, proteomics, and metabolomics), systems biology, and artificial intelligence on microbial biocontrol agent discovery, functional validation, and predictive design. Examples from cereal crops, legumes, and horticulture crops indicate that the application of beneficial microbial inoculants can significantly lower the burden of pests and diseases, enhance crop productivity, and fit perfectly within an integrated pest management system. Lastly, we critically analyze the main challenges preventing large-scale adoption, such as inconsistent field performance, limited microbial survival and competitiveness, and comparative regulatory frameworks across global markets. Ultimately, eco-smart microbial biocontrol combines mechanistic insights with omics-driven discovery, artificial intelligence (AI)- assisted prediction, advanced formulation strategies, and field-level validation, creating a strong, scalable, and environmentally friendly framework for resilient, low-input agricultural systems.},
}

*Rhizosphere
*Plant Diseases/prevention & control/microbiology
Pest Control, Biological/methods
Soil Microbiology
Plant Roots/microbiology
*Biological Control Agents
Microbiota
Multiomics
Crops, Agricultural/microbiology
Fungi
*Plants/microbiology

@article {pmid42809026,
year = {2026},
author = {Akanmu, AM},
title = {Beyond the Rumen: Current Evidence and Knowledge Gaps in Microbial Diversity and Function Across the Bovine Gastrointestinal Tract.},
journal = {Current microbiology},
volume = {83},
number = {11},
pages = {},
pmid = {42809026},
issn = {1432-0991},
mesh = {Animals ; Cattle/microbiology ; *Gastrointestinal Tract/microbiology ; Rumen/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Fermentation ; Biodiversity ; },
abstract = {The bovine gastrointestinal tract (GIT) is a spatially organised microbial ecosystem, but the evidence supporting a whole-tract interpretation is highly uneven. This critical review distinguishes well-established rumen biology from emerging observations in the reticulum, omasum, abomasum, small intestine and hindgut. Comparative studies show strong regional filtering of microbial communities, yet most available datasets are cross-sectional, use digesta rather than mucosa, and infer function from DNA. Consequently, the presence of genes or taxa cannot be equated with active metabolism. Early life provides an important developmental dimension: microbial succession during the milk-to-solid-feed transition accompanies rumen maturation and region-specific immune development, although durable effects on adult productivity remain incompletely demonstrated. Across adult cattle, foregut fermentation supplies most microbially derived energy, whereas downstream compartments support residual fermentation, epithelial interactions and barrier-related processes whose quantitative contributions are less certain. Methanogenesis is therefore treated as one outcome among nutrition, immune function, pathogen resistance and gut integrity. Metagenomics, metatranscriptomics, metaproteomics and metabolomics are complementary rather than interchangeable; coordinated sampling is required to connect functional potential to activity and host phenotype. Priority should be given to longitudinal, multi-compartment, mucosa-and-digesta studies with absolute microbial measurements, metabolite fluxes and transparent causal inference. A tract-wide framework is valuable not because all compartments are equally understood, but because it makes the present evidence imbalance explicit and identifies where microbiome-targeted nutrition can be tested responsibly.},
}

Animals
Cattle/microbiology
*Gastrointestinal Tract/microbiology
Rumen/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Fermentation
Biodiversity

@article {pmid42811337,
year = {2026},
author = {Detman-Ignatowska, A and Schiro, G and Filip, R and Samborowska, E and Karczmarski, J and Jarmakiewicz-Czaja, S and Jakubowska, K and Williams, A and Hickman, NR and Laubitz, D and Sikora, A},
title = {Fecal microbiota fermenting simple organic carbon substrates in vitro as microbial factories capable of distinguishing Crohn's disease from healthy states.},
journal = {Microbial cell factories},
volume = {25},
number = {1},
pages = {},
pmid = {42811337},
issn = {1475-2859},
support = {MG-2/21-18//Institute of Biochemistry and Biophysics Polish Academy of Sciences/ ; },
mesh = {Humans ; *Feces/microbiology ; Fermentation ; *Crohn Disease/microbiology/diagnosis ; Lactic Acid/metabolism ; Butyrates/metabolism ; *Gastrointestinal Microbiome ; Acetates/metabolism ; Bacteria/metabolism/classification ; Glucose/metabolism ; },
abstract = {BACKGROUND: Crohn's disease (CD) is characterized by low microbial richness and diversity of the gut microbiome, shifts in the abundance of specific taxa, reduced presence of C2-C6 organic acid producers, especially butyrate-forming bacteria, and alterations in gut metabolites. This study aimed to demonstrate differences in the dynamics and fermentation activity of the fecal microbiota of CD patients and healthy individuals (HIs) grown in vitro on glucose or a mixture of acetate and lactate (fecal microbiota batch cultures). Glucose was used as a substrate for glycolytic fermentation, whereas a mixture of acetate and lactate supported related pathways leading to the production of C2-C6 organic acids, particularly butyrate via the conversion of lactate and acetate.

RESULTS: HI fecal microbiota cultures produced butyrate mainly through lactate and acetate transformation rather than via glucose fermentation. This pathway was impaired in the CD fecal microbiota cultures, which exhibited reduced synthesis of butyrate, valerate, caproate and propionate, and excessive production of ethanol and certain amino acids. These distinct fermentation activities stemmed from differences in the original CD and HI fecal microbiota composition that were further accentuated in batch cultures. The number of beneficial commensal bacteria (e.g., Coprococcus catus, Ruminococcus torques, Gemmiger formicilis, Eubacterium rectale, Fusicatenibacter saccharivoransi, Faecalibacterium prausnitzii) were significantly lower in the CD fecal microbiota cultures and correlated with reduced butyrate, valerate and caproate levels. Conversely, an overabundance of the recognized CD dysbiosis-associated bacteria, such as Escherichia coli, was reflected in elevated ethanol and amino acid levels in post-fermentation liquids. Metabolic potential analysis further indicated an enrichment of genes encoding enzymes involved in ethanol and amino acid biosynthesis in CD fecal microbiota cultures and highlighted the metabolic versatility of E. coli.

CONCLUSIONS: Fermentation patterns of fecal microbiotas in batch cultures can distinguish CD-associated dysbiosis from a healthy microbiome, with particular emphasis on lactate and acetate conversion to butyrate as a key pathway of butyrate production. The differences are observed under standardized in vitro conditions without the need to reconstruct the intestinal environment. These findings, pending further validation, may offer novel diagnostic opportunities and have implications for strategies aimed at restoring a healthy gut microbiome.},
}

Humans
*Feces/microbiology
Fermentation
*Crohn Disease/microbiology/diagnosis
Lactic Acid/metabolism
Butyrates/metabolism
*Gastrointestinal Microbiome
Acetates/metabolism
Bacteria/metabolism/classification
Glucose/metabolism

@article {pmid42811876,
year = {2026},
author = {Bo, T and Liu, X and Liu, M and Shen, W and Zhang, X and Guo, H and Wen, J},
title = {Winter Caching of Artemisia frigida Is Associated With Host Physiological and Gut Microbial Variation in Brandt's Voles.},
journal = {Molecular ecology},
volume = {35},
number = {19},
pages = {e70576},
doi = {10.1111/mec.70576},
pmid = {42811876},
issn = {1365-294X},
support = {32470487//National Natural Science Foundation of China/ ; 32201278//National Natural Science Foundation of China/ ; 2023FY100305//Science & Technology Fundamental Resources Investigation Program/ ; 5242016//Natural Science Foundation of Beijing Municipality/ ; },
mesh = {Animals ; *Arvicolinae/physiology/microbiology/genetics ; Seasons ; *Artemisia ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Hypothalamus/metabolism ; Cold Temperature ; Transcriptome ; Lipid Metabolism/genetics ; },
abstract = {Seasonal variation in food resources represents a major ecological challenge for wild herbivores, yet how naturally selected dietary resources become associated with host and microbial responses remains poorly understood. During winter, Brandt's voles (Lasiopodomys brandtii) cache large amounts of Artemisia frigida, suggesting that this plant may have ecological significance beyond its nutritional value. However, the biological basis underlying this seasonal food preference remains unclear. Here, using Brandt's voles as a model system, we investigated whether the naturally selected winter food A. frigida was associated with coordinated variation in host physiology and gut microbial organization under cold conditions. By integrating physiological phenotyping, hypothalamic neuroendocrine analyses, adipose tissue transcriptomics, shotgun metagenomics and metagenomic binning, we characterized host and microbial responses across multiple biological levels. Dietary A. frigida was associated with altered hypothalamic AgRP expression, increased UCP1 expression in BAT and transcriptional changes related to lipid metabolism and thermogenic pathways during cold exposure. Supplement of A. frigida was associated with changes in gut microbial community structure, enrichment of specific bacterial taxa and shifts in predicted microbial functional potential. Genome-resolved analyses further reconstructed 277 non-redundant metagenome-assembled genomes, enabling assessment of microbial ecological variation associated with seasonal food conditions. Together, our findings provide molecular ecological evidence linking winter caching of A. frigida with coordinated variation in host physiology and gut microbial organization, highlighting seasonal dietary resources as an overlooked component of ecological variation in wildlife.},
}

Animals
*Arvicolinae/physiology/microbiology/genetics
Seasons
*Artemisia
*Gastrointestinal Microbiome/genetics
Metagenomics
Hypothalamus/metabolism
Cold Temperature
Transcriptome
Lipid Metabolism/genetics

@article {pmid42320811,
year = {2026},
author = {Wang, Y and Wu, X and Deng, H and Yan, G and Xu, Z and Zhu, L},
title = {A high-molecular-weight polysaccharide from Polygonatum sibiricum inhibits distant tumor growth associated with gut microbiota remodeling and Enhances with αPD-1 therapy.},
journal = {International journal of biological macromolecules},
volume = {377},
number = {},
pages = {153116},
doi = {10.1016/j.ijbiomac.2026.153116},
pmid = {42320811},
issn = {1879-0003},
mesh = {Animals ; *Polygonatum/chemistry ; *Polysaccharides/pharmacology/chemistry ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Molecular Weight ; Cell Line, Tumor ; Humans ; Immune Checkpoint Inhibitors/pharmacology ; Cell Proliferation/drug effects ; Female ; },
abstract = {BACKGROUND: Defined polysaccharide fractions can reshape the gut microbiome and influence systemic antitumor immunity. We investigated whether an operationally defined high-molecular-weight Polygonatum sibiricum polysaccharide fraction (PSP-H) enriched by 100 kDa ultrafiltration suppresses growth of subcutaneous MC38 tumors via microbiota-associated mechanisms and potentiates anti-PD-1 therapy.

MATERIALS AND METHODS: PSP-H was isolated by cascade ultrafiltration and compared with a total polysaccharide extract (PSP-T) and lower-MW fractions. We profiled fecal metagenomes, serum metabolites, tumor molecular readouts (immunoblotting; HDAC activity), and immunity. Fecal microbiota transplantation (FMT) tested the microbiota dependence and sufficiency of PSP-H-remodeled communities to transfer the immunometabolic phenotype. Combination with anti-PD-1 (RMP1-14) was evaluated.

RESULTS: PSP-H showed minimal direct cytotoxicity while suppressing tumor growth, selectively enriching butyrate-producing taxa (e.g., Lachnospiraceae) and elevating serum butyrate and inosine, with TNF-α reduced. In vitro, butyrate enhanced T-cell production of IFN-γ, IL-2 and granzyme-B and counteracted IFN-γ-induced PD-L1 expression. In vivo, PSP-H reduced tumor HDAC activity and increased histone acetylation while inducing adaptive STAT1/PD-L1 upregulation. FMT recapitulated the key metabolite/cytokine signature. PSP-H + anti-PD-1 synergistically increased intratumoral CD8[+] T cells and yielded superior tumor control versus monotherapy.

CONCLUSION: PSP-H is a defined microbiota-modulating adjuvant that engages a microbiome-butyrate-immune axis to restrain subcutaneous tumors and sensitizes them to PD-1 blockade by reprogramming systemic immunity while inducing targetable adaptive resistance.},
}

Animals
*Polygonatum/chemistry
*Polysaccharides/pharmacology/chemistry
*Gastrointestinal Microbiome/drug effects
Mice
*Programmed Cell Death 1 Receptor/antagonists & inhibitors
Molecular Weight
Cell Line, Tumor
Humans
Immune Checkpoint Inhibitors/pharmacology
Cell Proliferation/drug effects
Female

@article {pmid42410398,
year = {2026},
author = {Xiang, X and Zhu, Y and Wang, T and Cheng, K and Ming, Y},
title = {Association between salivary microbiota-related amino acid metabolic dysregulation and tacrolimus-induced gingival overgrowth following kidney transplantation.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {},
pmid = {42410398},
issn = {1472-6831},
support = {81771722//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Kidney Transplantation ; *Gingival Overgrowth/chemically induced/microbiology ; *Tacrolimus/adverse effects ; *Immunosuppressive Agents/adverse effects ; *Microbiota ; *Amino Acids/metabolism ; *Saliva/microbiology/metabolism ; Female ; Male ; Middle Aged ; Case-Control Studies ; Adult ; },
abstract = {BACKGROUND: Kidney transplant (KT) recipients require lifelong immunosuppressive therapy to prevent allograft rejection. Drug-induced gingival overgrowth (DIGO) is a notable adverse effect of tacrolimus, for which effective preventive or therapeutic strategies are lacking. Dysbiosis of the oral microbiota has been implicated as a major risk factor for DIGO. However, its mechanistic role remains poorly understood.

RESULTS: Twenty KT recipients with newly diagnosed DIGO while receiving tacrolimus were enrolled, along with 20 matched controls with stable graft function. Salivary samples were collected and subjected to metagenomic and untargeted metabolomic profiling. Taxonomic analysis revealed greater microbial heterogeneity in DIGO patients compared to more interconnected communities observed in controls. Periodontitis-associated taxon, including Porphyromonas gingivalis, were enriched in the DIGO group. Multiple differentially expressed microbial genes and metabolites were identified, predominantly enriched in disordered amino acid metabolic pathways. Key metabolites-such as L-proline, carnosine, choline, 5-aminolevulinic acid, and spermidine-showed strong associations with DIGO-related taxon.

CONCLUSION: A strong association was observed between salivary microbial composition, metabolic profiles, and DIGO. The identified microbiota and metabolite alterations suggest a potential link between amino acid metabolic dysregulation and gingival fibroblast-related pathways in DIGO. These findings provide new insights into the biological features of DIGO and offer a foundation for future mechanistic and therapeutic studies.},
}

Humans
*Kidney Transplantation
*Gingival Overgrowth/chemically induced/microbiology
*Tacrolimus/adverse effects
*Immunosuppressive Agents/adverse effects
*Microbiota
*Amino Acids/metabolism
*Saliva/microbiology/metabolism
Female
Male
Middle Aged
Case-Control Studies
Adult

@article {pmid42532775,
year = {2026},
author = {Nealon, NJ},
title = {Next-Generation Sequencing in Companion Animal Practice for Infectious Disease Diagnostics and Characterizing Normal Microbiomes.},
journal = {The Veterinary clinics of North America. Small animal practice},
volume = {56},
number = {6},
pages = {1323-1336},
doi = {10.1016/j.cvsm.2026.06.005},
pmid = {42532775},
issn = {1878-1306},
mesh = {Animals ; *High-Throughput Nucleotide Sequencing/veterinary/methods ; *Microbiota/genetics ; *Pets/microbiology ; *Communicable Diseases/veterinary/diagnosis/microbiology ; *Gastrointestinal Microbiome/genetics ; Cats ; },
abstract = {The purpose of this article is to review and compare the most common and emergent next-generation sequencing methodologies used in small animal veterinary practice, with a focus on their applications to bacterial diagnostics and assessment of the healthy gut microbiome. These methodologies include whole genome sequencing, amplicon sequencing, shotgun metagenomic sequencing, and transcriptomics. Understanding the benefits and limitations of each methodology will help small animal practitioners to make informed decisions for their patients and maximize the utility of each test as part of a complete patient health assessment.},
}

Animals
*High-Throughput Nucleotide Sequencing/veterinary/methods
*Microbiota/genetics
*Pets/microbiology
*Communicable Diseases/veterinary/diagnosis/microbiology
*Gastrointestinal Microbiome/genetics
Cats

@article {pmid42546794,
year = {2026},
author = {Li, S and Chen, T and Liu, J and Lu, K and Chen, X and Lin, L and Lin, Y},
title = {Enriched microplastic-associated biofilms exacerbate gut microbial dysbiosis and metabolic disruption in mice.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {408},
number = {},
pages = {128873},
doi = {10.1016/j.envpol.2026.128873},
pmid = {42546794},
issn = {1873-6424},
mesh = {Animals ; *Microplastics/toxicity ; *Biofilms/drug effects ; Mice ; *Dysbiosis/chemically induced ; *Gastrointestinal Microbiome/drug effects ; },
abstract = {Microplastics (MPs) and opportunistic pathogens are recognized as emerging environmental hazards, yet the health risks associated with mammalian exposure to biofilms enriched on MP surfaces remain poorly characterized. This study evaluated the characteristics of microbial biofilms enriched on MPs from aquatic and sediment matrices over 12 weeks and assessed their potential health impacts using a murine mammalian model. Metagenomic profiling showed that the enriched biofilms exhibited alterations in community composition, accompanied by an overrepresentation of genes associated with antibiotic resistance, iron acquisition, and virulence traits. In the murine model, dietary exposure to the MP-associated biofilms coincided with changes in host intestinal inflammatory markers and a distinct shift in the gut microbiota profile. Metabolomic analysis further revealed synchronous alterations in extracellular and fecal metabolite profiles, including profiles linked to secondary bile acid pathways, alongside a downregulation of intestinal barrier tight junction markers. These parallel taxonomic and metabolic shifts indicate that environmental biofilms enriched on microplastics can provoke complex physiological responses in a mammalian host. This study provides a valuable framework for assessing the potential mammalian health risks posed by plastisphere-associated microbial complexes.},
}

Animals
*Microplastics/toxicity
*Biofilms/drug effects
Mice
*Dysbiosis/chemically induced
*Gastrointestinal Microbiome/drug effects

@article {pmid42584101,
year = {2026},
author = {Yu, D and Zhang, L and Agu, D and Gao, N and Xiao, Y and Zhang, M and Zhang, J and Yan, J},
title = {Temporal succession of microbiomes and resistomes during buried rat carcass decomposition.},
journal = {mSphere},
volume = {11},
number = {9},
pages = {e0043726},
doi = {10.1128/msphere.00437-26},
pmid = {42584101},
issn = {2379-5042},
support = {82030058//National Natural Science Foundation of China/ ; 82101977//National Natural Science Foundation of China/ ; 202503021211157//Natural Science Foundation of Shanxi Province/ ; },
mesh = {Animals ; *Bacteria/classification/genetics/drug effects ; Gene Transfer, Horizontal ; Rats ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Interspersed Repetitive Sequences ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Burial is a prevalent approach for disposing of human and animal carcass. Carcass decomposition is a key natural disturbance that reshapes microbial communities and modulates biogeochemical cycles. Animal intestines serve as critical natural reservoirs of antibiotic resistance genes (ARGs), and carcass decomposition concurrently remodels intestinal bacterial assemblages and resistome profiles. Most previous studies have characterized microbial succession in surface-exposed carcasses, yet the coordinated temporal shifts of intestinal microbiota, resistomes, and horizontal gene transfer (HGT) signatures within buried carcasses remain underexplored. We established a buried rat carcass model and performed metagenomic sequencing to characterize temporal dynamics of intestinal bacteria, ARGs, mobile genetic elements (MGEs), and HGT events. Bacterial communities underwent directional succession accompanied by reduced α-diversity and stage-specific β-diversity. Proteobacteria gradually outcompeted Firmicutes and Bacteroidetes to become dominant taxa. The resistome followed regular temporal changes: tetracycline and macrolide-lincosamide-streptogramin (MLS) ARGs prevailed in early decomposition, while multidrug, β-lactam, polymyxin, and quinolone ARGs accumulated in mid-late stages, with ARG richness peaking on day 28. Approximately 83% of temporally dynamic ARG subtypes were positively correlated with decomposition duration. Procrustes analysis (R[2] = 0.859) revealed strong correlations between bacterial succession and resistome dynamics, with Proteobacteria as potential multidrug-resistant hosts and major HGT donors. This study identifies a correlative cascade of microbial succession that drives MGE functional shift, which in turn increased HGT potential and ultimately leads to resistome accumulation in buried carcass intestinal habitats. These findings expand the theoretical framework of disturbance-driven microbial-resistome co-succession and offer insights into drivers of antibiotic resistance propagation in terrestrial cadaver systems.IMPORTANCEAnimal carcass burial is a ubiquitous natural terrestrial disturbance, and carcass intestinal contents represent a major endogenous reservoir of environmental antibiotic resistance genes (ARGs). Although extensive research has characterized microbial succession of exposed carcasses, the co-occurrence patterns of gut microbiome and resistome together with associated horizontal gene transfer (HGT) under buried conditions remain underexplored. Using metagenomic profiling of decomposing rat intestinal feces, this study explores a potential correlative cascade spanning bacterial succession, mobile genetic element (MGE) functional shifts, increased HGT potential, and gradual ARG enrichment. Our findings expand the ecological data set focused on subsurface buried carcass habitats and advance mechanistic knowledge of coupled microbiome-resistome succession driven by postmortem decomposition.},
}

Animals
*Bacteria/classification/genetics/drug effects
Gene Transfer, Horizontal
Rats
*Gastrointestinal Microbiome/genetics
Metagenomics
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
Interspersed Repetitive Sequences
*Drug Resistance, Bacterial/genetics

@article {pmid42628675,
year = {2026},
author = {Wang, Y and Lin, T and Zhang, X and Li, K and Guo, Z and Li, E and Wu, X and Li, Y and Wu, D and Deng, Q and He, P},
title = {Associations of low-level multi-metal exposure with peripheral blood-based inflammatory indices and the mediating role of gut microbiota: evidence from lifestyle-standardized men.},
journal = {Environmental research},
volume = {308},
number = {Pt 1},
pages = {125539},
doi = {10.1016/j.envres.2026.125539},
pmid = {42628675},
issn = {1096-0953},
mesh = {Humans ; Male ; *Inflammation/blood/chemically induced ; *Gastrointestinal Microbiome/drug effects ; *Metals/blood/toxicity ; Adult ; Middle Aged ; *Environmental Exposure ; *Environmental Pollutants/blood ; Feces/microbiology ; Life Style ; },
abstract = {With improving environmental regulation and pollution control, low-level multi-metal exposure and its potential health impacts have received increasing attention. However, evidence on metal-related immune-inflammatory phenotypes and mechanisms at low-exposure ranges remains limited. We therefore evaluated the associations between low-level multi-metal exposure and peripheral blood-based inflammatory indices and further explored the mediation roles of gut microbiota. We enrolled 98 men from a centrally managed setting with relatively standardized diets and daily routines. After measuring plasma concentrations of multiple metals, we selected 8 immune-inflammatory-related non-essential metals. We calculated systemic immune-inflammation index (SII), systemic inflammation response index (SIRI), neutrophil-to-lymphocyte ratio (NLR), and derived NLR (dNLR) based on complete blood counts. Fecal microbial composition and functional potential were profiled using full-length 16S ribosomal RNA sequencing and shotgun metagenomics. We found that within low-exposure range, lead (Pb) and cadmium (Cd) were inversely associated with SII, NLR, and dNLR (β ≤ -0.22; PFDR ≤ 0.040), and the overall metal mixture was also inversely associated with these indices (β = -0.37, P = 0.020). Pb was associated with a lower abundance of Agathobaculum butyriciproducens SR79 (β = -0.48; PFDR = 0.026), which mediated 17-21% of the inverse associations of Pb with SII, NLR, and dNLR (PFDR ≤ 0.030). Metagenomic analyses further linked SR79 to signatures of polyamine biosynthesis (β ≥ 0.39; PFDR ≤ 0.032) and GDP-manno-heptose biosynthesis (β = 0.30; PFDR = 0.012). Overall, these results suggested that even at low-exposure range, Pb and Cd were associated with lower peripheral blood-based inflammatory indices, potentially reflecting altered peripheral inflammatory profiles. Gut microbiota features may partly mediate the associations between low-level Pb exposure and peripheral blood-based inflammatory indices.},
}

Humans
Male
*Inflammation/blood/chemically induced
*Gastrointestinal Microbiome/drug effects
*Metals/blood/toxicity
Adult
Middle Aged
*Environmental Exposure
*Environmental Pollutants/blood
Feces/microbiology
Life Style

@article {pmid42660466,
year = {2026},
author = {Hou, F and Xuan, Y and Liu, T and Jiang, Y and Bao, Y and Wu, T and Zhang, Y and Wu, J and Ren, M and Huang, B and Wang, Z and Han, M},
title = {Polystyrene nanoplastics exposure induces reproductive toxicity in male mice associated with the gut-liver/testis axis.},
journal = {Toxicology and applied pharmacology},
volume = {516},
number = {},
pages = {118022},
doi = {10.1016/j.taap.2026.118022},
pmid = {42660466},
issn = {1096-0333},
mesh = {Animals ; Male ; *Polystyrenes/toxicity ; *Liver/drug effects/metabolism/pathology ; *Testis/drug effects/pathology/metabolism ; Mice ; *Gastrointestinal Microbiome/drug effects ; Sperm Motility/drug effects ; *Microplastics/toxicity ; *Reproduction/drug effects ; *Nanoparticles/toxicity ; Transcriptome/drug effects ; Dose-Response Relationship, Drug ; Dysbiosis/chemically induced ; },
abstract = {Environmental nanoplastics are increasingly prevalent in global environments and represent an emerging systemic health risk, yet the mechanistic links between nanoplastic exposure and multi-organ dysfunction in mammals remain incompletely characterized. We integrated phenotypic assessments, gut shotgun metagenomics, and dual-organ transcriptomics to investigate the toxic effects of 28-day oral exposure to polystyrene nanoplastics (PS-NPs) in male CD-1 mice. PS-NPs induced a non-monotonic dose-dependent response, characterized by significant body weight loss at high doses, severe impairment of sperm motility, and progressive epididymal histopathological lesions. Gut metagenomics revealed significant microbiota dysbiosis, including an elevated Firmicutes/Bacteroidota ratio and marked depletion of beneficial commensal bacteria such as Ligilactobacillus murinus. Hepatic transcriptomics identified dysregulation of metabolic, detoxification, and circadian rhythm pathways, while testicular transcriptomics identified sustained transcriptional downregulation of genes annotated to steroid hormone biosynthesis and alterations in FoxO and apoptosis-related signaling. Spearman correlation network analysis identified associations between specific microbial shifts and organ-specific transcriptional alterations, providing a hypothesis-generating framework for the proposed gut-liver/testis axis. Together, these findings indicate that, under the present experimental conditions, oral PS-NPs exposure was associated with gut microbial dysbiosis, hepatic transcriptional perturbations, reduced sperm motility, and epididymal histopathological alterations, while the mechanistic relationships among these changes require further experimental validation.},
}

Animals
Male
*Polystyrenes/toxicity
*Liver/drug effects/metabolism/pathology
*Testis/drug effects/pathology/metabolism
Mice
*Gastrointestinal Microbiome/drug effects
Sperm Motility/drug effects
*Microplastics/toxicity
*Reproduction/drug effects
*Nanoparticles/toxicity
Transcriptome/drug effects
Dose-Response Relationship, Drug
Dysbiosis/chemically induced

@article {pmid42696789,
year = {2026},
author = {Kan, Y and Fu, Y and Yang, W and Harindintwali, JD and Liu, Q and Jiang, X and Wang, C and Hu, J and Chen, L and Wang, C and Tian, D and Ye, M and Jiang, X},
title = {Rhizosphere microbiome assembly and functional enrichment drive salt tolerance in wheat.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130869},
doi = {10.1016/j.jenvman.2026.130869},
pmid = {42696789},
issn = {1095-8630},
mesh = {*Triticum/physiology/microbiology ; *Rhizosphere ; *Microbiota ; *Salt Tolerance ; *Soil Microbiology ; Soil/chemistry ; RNA, Ribosomal, 16S ; },
abstract = {Soil salinization is a major constraint on wheat production, as seedling-stage stress strongly constrains early growth and potential yield. However, the mechanisms by which the rhizosphere microbiome mediates varietal differences in salt tolerance remain poorly understood. Here, we compared a salt-tolerant wheat cultivar (Jimai60, JM60) and a salt-sensitive cultivar (Guomai301, GM301) grown in saline-alkali soil. Integrating soil physicochemical, enzymatic analyses and 16S rRNA gene and shotgun metagenomic sequencing, we investigated rhizosphere microbiome assembly, network structure, and functional potential at the seedling stage. JM60 assembled a distinct rhizosphere microbiome enriched in Bacteroidota, with Sphingobacterium acting as a keystone taxon in a more stable co-occurrence network. In contrast, GM301 was dominated by Zobellella and exhibited increased negative microbial interactions, indicating a reduced network that is structurally more cooperative. Metagenomic analyses showed enrichment in JM60-associated microbiomes of genes linked to oxidative stress resistance (katE), central carbon metabolism (pdhD), and nitrogen utilization (hutF), suggesting enhanced redox homeostasis, nutrient cycling, and ion balance regulation. These functional traits aligned with higher leaf antioxidant enzyme activity and altered rhizosphere nutrient profiles in JM60. Our findings demonstrate that wheat salt tolerance is linked to assembly of a functionally enriched rhizosphere microbiome, highlighting microbiome-driven mechanisms for improving crop resilience in saline soils.},
}

*Triticum/physiology/microbiology
*Rhizosphere
*Microbiota
*Salt Tolerance
*Soil Microbiology
Soil/chemistry
RNA, Ribosomal, 16S

@article {pmid42700527,
year = {2026},
author = {Yin, Z and Ping, H and Li, C},
title = {Antimony species-dependent enrichment and transcriptional activity of antibiotic and metal resistance genes in the gut microbiome of male mice.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130867},
doi = {10.1016/j.jenvman.2026.130867},
pmid = {42700527},
issn = {1095-8630},
mesh = {Animals ; *Antimony ; Mice ; Male ; *Gastrointestinal Microbiome/drug effects/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The gut microbiome is a reservoir for antibiotic resistance genes (ARGs) and is sensitive to environmental pollutants. ARGs in environmental and host-associated microbiomes can be enriched by metal(loid)s through co-selection with metal resistance genes (MRGs). However, as a ubiquitous toxic metalloid, antimony (Sb) induced alterations of ARGs in the gut microbiome and the underlying mechanisms remain unclear. Here, by integrating genome-resolved metagenomics and metatranscriptomics, we characterized the genomic potential and transcriptional activity of ARGs and MRGs in the gut microbiome of mice exposed to Sb(III)- and Sb(V)-contaminated drinking water. We found that both Sb(III) and Sb(V) significantly increased ARGs abundance, whereas only Sb(III) enhanced ARGs transcription (288.40 ± 41.67 TPM, P < 0.05). Co-selection of ARGs and MRGs was observed through metagenome-assembled genomes (MAGs) analysis, and key taxa driving this process were identified (e.g., Eubacterium_J and Lachnospiraceae_COE1). Sb(III), but not Sb(V), induced co-regulation of macrolide-lincosamide-streptogramin resistance genes and arsRABC operon. A potentially higher risk of ARG dissemination under Sb(III) stress was suggested by the increased abundance and transcription of mobile genetic elements (MGEs). This study advances our understanding of the interactions between Sb and ARGs in the gut microbiome and highlights the potential chemical species-dependent enrichment and transcriptional activation of ARGs.},
}

Animals
*Antimony
Mice
Male
*Gastrointestinal Microbiome/drug effects/genetics
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology

@article {pmid42767155,
year = {2026},
author = {Xu, P and Li, L and Zhang, Y and Jiang, Q and Zhang, Y and Wu, X and Xu, Y},
title = {Threshold effects of organic amendment on acidic red soil remediation: Community assembly and core microbiome-mediated metabolic coupling.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130999},
doi = {10.1016/j.jenvman.2026.130999},
pmid = {42767155},
issn = {1095-8630},
mesh = {*Soil/chemistry ; *Soil Microbiology ; *Microbiota ; Biodegradation, Environmental ; Metagenome ; },
abstract = {To identify the ecological threshold and microbial mechanisms underlying organic amendment (OA)-mediated remediation of acidic red soils, pak choi was employed as a model plant, and a gradient of digestate-derived OA from 0% to 25% was established. This study integrated soil-plant assessment, community assembly modeling, metagenome-assembled genomes (MAGs), and metabolic network analysis. Both soil functioning and plant growth exhibited nonlinear responses. The optimal OA rate was found to be 15%, which increased the soil quality index and pak choi biomass by 92% and more than 13-fold compared to the control group. In contrast, a 25% OA rate elevated electrical conductivity, induced secondary salinity stress, and reduced productivity and economic returns. Under the 15% OA treatment, the microbial community showed the strongest deviation from neutral community model predictions, indicating that neutral processes had limited explanatory power for community assembly, while deterministic processes associated with altered soil conditions may have played a more important role in community reorganization. Accordingly, core functional MAGs (e.g., MAG302, MAG299, MAG321) were significantly enriched under this treatment, with a total relative abundance 17.3 times that of the control group. These MAGs harbored key genes involved in C, N, P, and S cycling (bglB, atoB, narG, nirK, nosZ, gcd, pst, sqr), suggesting functional complementarity in organic matter degradation, denitrification, phosphorus mobilization, and sulfide oxidation, thereby supporting efficient nutrient turnover and system function. Deviation from this threshold resulted in reduced core MAG enrichment and metabolic network synergy. Overall, this study provides genome-resolved targets for functional strain isolation and synthetic community construction, as well as a mechanistic basis for optimizing OA rates and developing microbiome-based precision remediation strategies.},
}

*Soil/chemistry
*Soil Microbiology
*Microbiota
Biodegradation, Environmental
Metagenome

@article {pmid42804444,
year = {2026},
author = {Kirtane, A and van der Loo, E and Doppmann, Z and Deiner, K},
title = {Distinct Environmental DNA States Reveal Biodiversity and Transport Patterns Across Alpine Watersheds.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70207},
pmid = {42804444},
issn = {1755-0998},
support = {852621//H2020 European Research Council/ ; },
mesh = {*DNA, Environmental/genetics/isolation & purification ; *Biodiversity ; Animals ; Extrachromosomal DNA ; Lakes ; *Rivers/chemistry ; Plants/genetics/classification ; DNA Barcoding, Taxonomic ; Metagenomics/methods ; },
abstract = {Environmental DNA (eDNA) exists in three states: membrane-bound, adsorbed and dissolved. These states differ in persistence and degradation, strongly influencing the interpretation of eDNA data. Despite this, they have rarely been separated and analyzed independently from environmental samples. We developed a state-sorting workflow to isolate and analyze them, applying it to samples from 221 sites from 58 streams across eight lake watersheds with COI and ITS metabarcoding, targeting metazoans and plants, respectively, to reveal differences in biodiversity content and transport dynamics. Our results show that all three states contain both shared and unique taxonomic diversity of metazoan eDNA. However, the plant eDNA was only detected in the membrane-bound state. For metazoans, membrane-bound eDNA contained 87.8% of observed ASVs, far exceeding the adsorbed (37.2%) and dissolved (20.5%) states. Only membrane-bound eDNA showed evidence of downstream transport, but its extent varied among watersheds due to local hydrology. While upstream eDNA was transported to stream-lake confluences, lake surface samples showed a turnover in community composition. Clarifying the fate of membrane-bound eDNA within lakes will enhance catchment-level detection from lake samples and understanding of lake hydrodynamics. Of the environmental parameters assessed, water temperature was most strongly aligned with changes in community composition between sites. Most previous studies have likely captured the majority of the eDNA diversity within their samples by inadvertently targeting the membrane-bound state. This study demonstrates the utility of eDNA state-sorting, but the methods require further refinement. Analyzing states independently improves the interpretation of eDNA data and elucidates the processes governing eDNA fate and transport.},
}

*DNA, Environmental/genetics/isolation & purification
*Biodiversity
Animals
Extrachromosomal DNA
Lakes
*Rivers/chemistry
Plants/genetics/classification
DNA Barcoding, Taxonomic
Metagenomics/methods

@article {pmid42804599,
year = {2026},
author = {Hensen, T and Khatib, L and Patel, L and McDonald, D and González, A and MahmoudianDehkordi, S and Blach, C and Knight, R and Kaddurah-Daouk, R and Thiele, I},
title = {Personalized whole-body modeling links gut microbiota to metabolic perturbations in Alzheimer's disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2732659},
doi = {10.1080/19490976.2026.2732659},
pmid = {42804599},
issn = {1949-0984},
mesh = {Humans ; *Alzheimer Disease/microbiology/metabolism/blood ; *Gastrointestinal Microbiome ; Male ; Female ; Aged ; Bacteria/classification/isolation & purification/genetics/metabolism ; Cognitive Dysfunction/metabolism/microbiology ; Aged, 80 and over ; Metabolome ; },
abstract = {The human gut microbiome has been linked to metabolic disturbances in Alzheimer's disease (AD). However, the mechanisms by which gut microbes might influence metabolic dysfunction in AD remain poorly understood. Previously, gut microbiome-personalized whole-body models of human metabolism have been applied to predict how altered gut microbiome compositions may influence metabolites in the blood of healthy aging individuals with increased risk of AD. However, these previous results have not been validated in AD. In this study, we aimed to test these prior predictions in a cohort of AD dementia patients and individuals with mild cognitive impairment (MCI) and a probable AD diagnosis. Therefore, we created gut microbiome-personalized whole-body metabolic models for 34 AD dementia patients, 51 MCI patients, and 298 healthy controls. These in silico models were profiled to predict the metabolic influences of gut microbiomes on blood metabolites with previously reported alterations in AD. We found increased capacities of the in silico host-microbiome co-metabolism to produce S-adenosyl-L-methionine, L-arginine, creatine, taurine, and formate in the blood of AD patients. The metabolic predictions were then linked to key microbial taxa using a novel method that combines modeling-informed prediction sensitivity to alternative microbial abundances with LASSO-based taxonomic stability selection and elastic net regressions. This method found that increased relative abundances of Bacteroides uniformis and Bacteroides thetaiotamicron in AD were major factors driving the predicted metabolic changes. Furthermore, the metabolic predictions were associated with allelic variations in the APOE risk gene in healthy individuals, confirming our previous findings. In conclusion, we identified blood metabolites with known links to AD that were differentially influenced by gut microbiota in AD, and identified possible microbial drivers of these predicted shifts in host-microbiome interactions. These findings may facilitate the development of microbiome-informed treatments of AD.},
}

Humans
*Alzheimer Disease/microbiology/metabolism/blood
*Gastrointestinal Microbiome
Male
Female
Aged
Bacteria/classification/isolation & purification/genetics/metabolism
Cognitive Dysfunction/metabolism/microbiology
Aged, 80 and over
Metabolome

@article {pmid42806173,
year = {2026},
author = {Balasubramaniyan, M and Karthik, PA and Veeran, Y},
title = {Predicted shifts in microbial functional potential across the late glacial to holocene transition: a 16S rRNA-based inference from southeastern Arabian Sea sediments.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {10},
pages = {},
pmid = {42806173},
issn = {1572-9699},
mesh = {*Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; *Microbiota/genetics ; Phylogeny ; Seawater/microbiology ; *Archaea/genetics/classification/metabolism ; },
abstract = {Marine sediments preserve valuable records of ancient microbial communities. In this exploratory study, direct environmental amplicon sequencing reconstruction is often constrained by DNA degradation. In this exploratory study, we applied predictive functional profiling (PICRUSt2) to 16S rRNA gene amplicon data from five discrete sediment horizons spanning ~14.400 years (Bølling-Allerød, Younger Dryas, Early Holocene, Mid-Holocene, and Late Holocene) in the southeastern Arabian Sea. Inferred functional profiles based on Clusters of Orthologous Groups (COGs) pointed to variations in the predicted abundance of genes associated with carbon metabolism-specifically COG0183 (Acetyl-CoA acetyltransferase) and COG1024 (Enoyl-CoA hydratase/carnitine racemase)-and transport systems. Notably, the predicted potential for carbon metabolism reached its peak during the early Holocene, suggesting possible changes in carbon cycling dynamics during this warming phase. Principal component analysis accounted for 68.7% of the variance in predicted functions across time periods. While these findings are predictive and rely on amplicon-based inference, they provide a preliminary model of microbial functional reorganisation during major climate transitions, offering hypotheses for future high-resolution metagenomic validation.},
}

*Geologic Sediments/microbiology
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/metabolism
*Microbiota/genetics
Phylogeny
Seawater/microbiology
*Archaea/genetics/classification/metabolism

@article {pmid42047611,
year = {2026},
author = {Capone, K and Kuller, J and Durand, DJ and Tierney, NK and Lund, C},
title = {Exploration of Changes in the Human Skin Microbiome by Mode of Birth and Following First Bath.},
journal = {Pediatric dermatology},
volume = {43},
number = {5},
pages = {1046-1053},
doi = {10.1111/pde.70219},
pmid = {42047611},
issn = {1525-1470},
support = {UL1 TR000004/TR/NCATS NIH HHS/United States ; //Johnson & Johnson Consumer Inc./ ; UL1 TR000004//National Center for Advancing Translational Sciences, National Institutes of Health/ ; },
mesh = {Humans ; *Skin Microbiome ; Female ; *Baths ; Infant, Newborn ; *Cesarean Section ; *Delivery, Obstetric/methods ; Male ; *Skin/microbiology ; Pregnancy ; RNA, Ribosomal, 16S ; *Microbiota ; },
abstract = {BACKGROUND/OBJECTIVES: Microbes colonize the skin soon after birth, and the skin microbiome changes over time. However, the effects of bathing and hygiene products on the infant skin microbiome are not well studied. This randomized, single-center trial analyzed the skin microbiome in neonates born vaginally or via cesarean section (c-section), before and after their first bath with or without a mild baby cleanser.

METHODS: One hundred healthy full-term neonates were randomized to baths with water alone or with mild baby cleanser, stratified by delivery mode. Volar forearm swabs of neonates (before and after first bath) and their mothers were analyzed by 16S rRNA metagenomic sequencing.

RESULTS: At birth, neonates born vaginally had greater overall richness of the skin microbiome versus those born via c-section. Vaginally delivered neonates had similar species richness as their mothers, while neonates delivered via c-section had much lower species richness. Shannon diversity was similar regardless of birth mode, but community structure varied. Species richness was similar before and after bath in vaginally delivered neonates, but those born via c-section had higher species richness after their first bath and showed larger changes in community structures, compared with the vaginal group. Whether water alone or baby cleanser was used for the first bath did not greatly affect skin microbiome composition.

CONCLUSIONS: The mode of birth had the largest effect on the skin microbiome composition, richness, and structure. Neonates born via c-section showed the largest post-bath changes in the skin microbiome, while the use of water or baby cleanser had little effect.},
}

Humans
*Skin Microbiome
Female
*Baths
Infant, Newborn
*Cesarean Section
*Delivery, Obstetric/methods
Male
*Skin/microbiology
Pregnancy
RNA, Ribosomal, 16S
*Microbiota

@article {pmid42387479,
year = {2026},
author = {Vastolo, A and Tolone, M and Gannuscio, R and Staropoli, A and Giosa, D and Bonomo, A and Vinale, F and Cutrignelli, MI and Todaro, M},
title = {Impact of Opuntia spp. by-product silage on sheep metabolic profile, rumen fermentation and microbial communities.},
journal = {BMC veterinary research},
volume = {22},
number = {1},
pages = {},
pmid = {42387479},
issn = {1746-6148},
support = {cod. U-Gov PRJ-1776; CUP: J83C22000830005//National Recovery and Resilience Plan (PNNR) of Italy: project Biometric-Call PNNR a cascata-Università della TUSCIA/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; Female ; Fermentation ; *Opuntia ; *Silage/analysis ; Sheep/metabolism/microbiology ; Diet/veterinary ; Metabolome ; Animal Feed/analysis ; Fatty Acids, Volatile/analysis/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animal Nutritional Physiological Phenomena ; },
abstract = {BACKGROUND: Prickly pear (Opuntia ficus-indica) by-products represent a promising alternative feed resource for improving the sustainability of sheep production systems in Mediterranean areas. This study evaluated the effects of prickly pear by-product (PPB) silages on rumen fermentation, metabolic profile, and rumen microbiome in lactating ewes. Twelve Valle del Belice ewes were assigned to three dietary treatments (control, CTR; prickly pear peel silage, PPP; and pastazzo silage, PPS) in a Latin square design. Blood biochemical parameters, rumen volatile fatty acids (VFA), and metagenomic profiles were analysed.

RESULTS: PPB inclusion did not induce significant changes in blood biochemical parameters, which remained within physiological ranges. Rumen fermentation parameters were significantly affected, with the PPP diet increasing total VFA concentration and promoting a more glucogenic profile through higher propionate production. The rumen microbiome was dominated by Prevotella, which showed higher relative abundance in the CTR diet. PPB supplementation was associated with shifts in microbial functional profiles, including pathways related to polyphenol degradation, vitamin K2 biosynthesis, and central carbon metabolism, partially consistent with observed changes in rumen fermentation. No significant effects were observed on methanogenesis-related pathways.

CONCLUSIONS: Prickly pear by-product silages, particularly prickly pear peel, modulate rumen fermentation and microbial functional profiles in lactating ewes without adversely affecting systemic metabolic status.},
}

Animals
*Rumen/microbiology/metabolism
Female
Fermentation
*Opuntia
*Silage/analysis
Sheep/metabolism/microbiology
Diet/veterinary
Metabolome
Animal Feed/analysis
Fatty Acids, Volatile/analysis/metabolism
*Gastrointestinal Microbiome/drug effects
Animal Nutritional Physiological Phenomena

@article {pmid42801100,
year = {2026},
author = {Robinson, DM and Li, W and Breitbart, M and Takacs-Vesbach, C and Priscu, JC},
title = {Bacteriophages in Antarctic subglacial lakes reveal novel biodiversity and biogeochemical potential.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag252},
pmid = {42801100},
issn = {2730-6151},
abstract = {Of the more than 600 subglacial lakes identified in Antarctica thus far, Whillans Subglacial Lake and Mercer Subglacial Lake are the only lakes to have been directly and cleanly sampled. Although hydrologically isolated from direct marine contact for approximately 6.3 ± 1.0 ka, both lakes periodically discharge into the Ross Ice Shelf marine cavity. We present the first direct characterization of bacteriophages in Antarctic subglacial lakes, combining microscopy, metagenomics, and gene-sharing network analyses with bacteriophages found in the Ross Ice shelf marine cavity. The data reveal that bacteriophages are less abundant than their microbial hosts, with virus to prokaryote ratios below those of typical oligotrophic environments. Eight hundred sixty-one double-stranded DNA viral contigs were recovered forming 66 distinct viral clusters; only 18.4% could be identified at ≥85% sequence similarity in the IMG/VR database, showing high genetic novelty. The data showed 114 putative auxiliary metabolic genes involved in nutrient cycling and DNA methylation, and we predicted hosts spanning 13 prokaryotic classes. Several genetic clusters were shared with Antarctic subglacial lakes and Ross Ice Shelf cavity, indicating ecological connectivity that may extend the influence of subglacial phages to carbon and nutrient cycling in downstream Antarctic coastal ecosystems.},
}

@article {pmid42802107,
year = {2026},
author = {Beeby, N and Rasoanarimalala, C and Rasoavolandrainy, MF and Rothman, JM and Higham, JP and Sardaro, MLS and Amato, KR and Webster, TH and Baden, AL},
title = {Microbial and Metabolic Flexibility in Response to Habitat Disturbance in an Ecologically Specialist Primate.},
journal = {Molecular ecology},
volume = {35},
number = {18},
pages = {e70562},
doi = {10.1111/mec.70562},
pmid = {42802107},
issn = {1365-294X},
mesh = {Animals ; *Ecosystem ; Diet ; Forests ; *Gastrointestinal Microbiome/genetics ; *Strepsirhini/microbiology/metabolism/physiology ; RNA, Ribosomal, 16S/genetics ; Energy Metabolism ; Lemuridae ; },
abstract = {In the Anthropocene, understanding what renders a species prone to extinction is critical to wildlife management. Ecological specialists are hypothesised to be at particular risk, given that morphological, physiological, and/or behavioural constraints are expected to impede their responses to rapid habitat degradation. Nevertheless, studies have found mixed support for this hypothesis, raising the question, 'how resilient are specialists to environmental change?' Here, we test the hypothesis that ecological specialists, limited by behavioural and physiological constraints, may be at an energetic disadvantage in degraded habitats. Specifically, we tested whether Critically Endangered dietary specialist primates, black-and-white ruffed lemurs (Varecia variegata), living in secondary forests suffered nutritional and energetic deficits compared to those in primary forest habitats over a 12-month period. To do this, we used mixed modelling approaches to examine relationships among behaviour, nutritional chemistry, 16S sequencing, metagenome functional predictions, metabolite profiles, and energetic outcomes. Compared to primary forest-living conspecifics, we found that animals in the degraded forest consumed slightly fewer calories from less diverse diets. These animals exhibited less diverse gut microbiota, reduced microbial functional potential, and altered metabolomic profiles. Nevertheless, despite apparent nutritional constraints, energetic outcomes were broadly similar across habitats. These findings suggest that an organism's gut microbiome may be able to regulate microbial metabolic potential to facilitate resilience under suboptimal conditions. These findings highlight host-microbiome interactions as an important component of resilience in ecological specialists, with broad implications for predicting species persistence amid ongoing environmental change.},
}

Animals
*Ecosystem
Diet
Forests
*Gastrointestinal Microbiome/genetics
*Strepsirhini/microbiology/metabolism/physiology
RNA, Ribosomal, 16S/genetics
Energy Metabolism
Lemuridae

@article {pmid42803857,
year = {2026},
author = {Ali, S and Ali, B and Shaukat, A and Alghamdi, S and Kabrah, A and Ahmed, MA and Zhang, L},
title = {From dysbiosis to disease: the role of gut microbial communities in Toxoplasma gondii pathogenesis, zoonotic transmission, diagnostic innovation, and therapeutic outcomes.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42803857},
issn = {1573-7446},
mesh = {Animals ; *Dysbiosis/veterinary/parasitology/microbiology ; *Gastrointestinal Microbiome ; *Toxoplasma/physiology ; *Zoonoses/transmission/parasitology/microbiology ; Humans ; *Toxoplasmosis, Animal/transmission/microbiology/diagnosis ; *Toxoplasmosis/transmission/therapy/microbiology/diagnosis/parasitology ; },
abstract = {Toxoplasma gondii, an obligate intracellular protozoan infecting approximately one-third of the global human population, causes substantial morbidity in immunocompromised individuals, congenital complications, neuropsychiatric sequelae, and considerable economic losses in livestock production. Gut microbial communities critically modulate T. gondii infection susceptibility, disease progression, and clinical outcomes, positioning the microbiome as a central axis in toxoplasmosis pathogenesis. This review examines the bidirectional relationship between gut microbiota and T. gondii, wherein dysbiosis functions simultaneously as a consequence and driver of disease severity. Protective commensal taxa reinforce intestinal barrier integrity, produce short-chain fatty acids, and stimulate anti-parasitic immunity through IFN-γ, IL-12, and tryptophan-aryl hydrocarbon receptor signaling, while pathobionts exacerbate immunopathology via TLR4 and inflammasome activation. Conversely, acute infection drives rapid microbial community collapse with persistent Proteobacteria expansion, butyrate-producing taxa depletion, neuroinflammation, and cognitive impairment in chronic infection. Across the One Health spectrum, host-specific microbiome signatures in felids, livestock, wildlife, and environmental reservoirs modulate zoonotic transmission dynamics and population-level susceptibility. Diagnostically, emerging microbiome-based approaches including metagenomics and multi-omics platforms offer promising biomarker discovery opportunities, though validated clinical signatures remain absent. Microbiome-targeted therapeutic strategies including probiotics, prebiotics, fecal microbiota transplantation, and postbiotics show preclinical promise, although human clinical trial validation is critically lacking. Critical research gaps and interdisciplinary One Health priorities are identified to advance microbiome-informed surveillance, diagnosis, and treatment of toxoplasmosis.},
}

Animals
*Dysbiosis/veterinary/parasitology/microbiology
*Gastrointestinal Microbiome
*Toxoplasma/physiology
*Zoonoses/transmission/parasitology/microbiology
Humans
*Toxoplasmosis, Animal/transmission/microbiology/diagnosis
*Toxoplasmosis/transmission/therapy/microbiology/diagnosis/parasitology

@article {pmid42804018,
year = {2026},
author = {Ren, G and Yang, W and Wang, J and Zhang, J and Gao, H and Gao, X and Chen, X and Wang, T and Cao, L and Wang, Z and Xiao, W},
title = {Longxue tongluo capsule enhances ischemic stroke recovery via microbiota-metabolite-gene interactions.},
journal = {Metabolic brain disease},
volume = {41},
number = {1},
pages = {},
pmid = {42804018},
issn = {1573-7365},
support = {JCYJ2326//Lianyungang Science and Technology Bureau/ ; JSTJ-2025-858//Young Elite Scientists Sponsorship Program by Jiangsu Province/ ; LYG06521202221//The sixth phase of the 521 Project scientific research funding project of Lianyungang/ ; BK20232014//Basic Research Program Natural Science Fund -Frontier Leading Technology Basic Research Special Project of Jiangsu Province/ ; },
mesh = {Animals ; *Ischemic Stroke/drug therapy/metabolism/genetics ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Recovery of Function/drug effects ; Male ; Brain/drug effects/metabolism ; *Brain Ischemia/drug therapy/metabolism ; Rats ; },
abstract = {The gut-brain axis represents an emerging therapeutic target. This study seeks to investigate the regulatory effects of LXTL on the brain-gut axis and to elucidate its mechanism of action during the ischemic stroke recovery period. This study investigated the effects of LXTL on a middle cerebral artery occlusion and reperfusion model. The assessment of recovery effects was conducted through the evaluation of brain injury scores, Y-maze performance, open field tests. Furthermore, comprehensive analyses were conducted on the gut microbiota, damaged brain tissue, cecal contents, and brain samples using metagenomic sequencing, transcriptomic sequencing, and non-targeted metabolomics. And the selected targets were verified. Integrated analyses were conducted by constructing correlation networks and performing joint pathway enrichment to elucidate the connections between microbial alterations, metabolite changes, and gene expression modifications. LXTL improved cognitive and exploratory behaviors, reduced brain damage and neuron loss, and enhanced gut health by increasing beneficial bacteria like Eubacterium and Kurthia. It boosted SCFAs, neuroactive metabolites, and altered nucleotide metabolism. LXTL is linked to genes involved in neurorepair and immune homeostasis, correlates with microglial polarization, and is associated with genes such as Ngfr, Card9, Chat, Nkg7, and Gch1 within the pertinent pathways. The integrated network linked LXTL-enhanced microbiota, gut and brain metabolites, and repair genes, facilitating recovery through a neurorepair-immune-metabolic triad. LXTL aids ischemic stroke recovery by altering gut microbiota and gut-brain metabolite profiles, while regulating brain gene networks related to neuroplasticity, inflammation, and metabolism. This demonstrates LXTL's multi-target effects through the gut-brain axis, underscoring the potential of herbal medicine in stroke rehabilitation.},
}

Animals
*Ischemic Stroke/drug therapy/metabolism/genetics
*Drugs, Chinese Herbal/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects
*Recovery of Function/drug effects
Male
Brain/drug effects/metabolism
*Brain Ischemia/drug therapy/metabolism
Rats

@article {pmid42799756,
year = {2026},
author = {Westerbeke, FHM and Warmbrunn, MV and Rios-Morales, M and Li, XS and Tian, MY and Novak, MA and Williams, AM and Hazen, SL and Attaye, I and Nieuwdorp, M},
title = {Plasma indole-3-propionic acid is a gut-derived metabolite and is associated with type 2 diabetes and cardiometabolic outcomes: Evidence from a human antibiotic intervention.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2736321},
doi = {10.1080/19490976.2026.2736321},
pmid = {42799756},
issn = {1949-0984},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/blood/metabolism/drug therapy ; *Indoles/blood ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; Male ; Female ; Middle Aged ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification/metabolism/drug effects ; Adult ; Propionates ; },
abstract = {The gut microbiota influences host metabolism through diverse metabolites, many of which have been linked to glucose homeostasis and type 2 diabetes (T2D). Understanding microbial contributions to metabolite biosynthesis is essential for developing dietary and microbiota-targeted T2D prevention and treatment strategies. We performed targeted plasma metabolomics in individuals with T2D and healthy controls, all receiving histidine supplementation, before and after gut microbiota suppression using 7-day broad-spectrum antibiotic treatment. Associations between pre-antibiotic metabolite levels and fecal metagenomics-derived gut microbiota composition were examined using co-abundance network analysis and Random Forest modeling. Indole-3-propionic acid (IPA) was the only gut-derived metabolite differing between groups before antibiotics, with lower levels in T2D and higher levels associated with reduced T2D odds. Antibiotic treatment reduced IPA to near-undetectable levels in both groups, confirming its predominantly microbial origin. Beyond established inverse associations with BMI and glycemic markers, we found a novel inverse correlation between IPA and glycemic variability, consistent with a protective association with T2D. Plasma IPA was associated with gut microbiota beta diversity. IPA-associated species clustered within a single co-abundance module, but did not include known IPA producers, suggesting plasma IPA is influenced by broader microbial community composition rather than IPA-producing capacity of individual taxa alone. This study provides direct human evidence that plasma IPA is virtually exclusively gut microbiota-derived in individuals with T2D, extending prior findings in healthy populations. It highlights IPA's relevance to metabolic health and T2D, and guides future research on dietary and microbiota-targeted strategies to modulate IPA, advancing T2D prevention and treatment.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/blood/metabolism/drug therapy
*Indoles/blood
*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/administration & dosage/therapeutic use
Male
Female
Middle Aged
Feces/microbiology
Bacteria/classification/genetics/isolation & purification/metabolism/drug effects
Adult
Propionates

@article {pmid42799757,
year = {2026},
author = {Zhang, J and Cao, X and Baniakina, LFT and Chai, L},
title = {Exploring biochar-mediated remediation of tetracycline-contaminated soil via a metagenomic approach: insights into soil microbial community and potential functions.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42799757},
issn = {1432-072X},
mesh = {*Charcoal/chemistry ; *Soil Microbiology ; *Tetracycline/pharmacology/metabolism ; Metagenomics ; *Bacteria/genetics/classification/drug effects/isolation & purification/metabolism ; *Soil Pollutants/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects/genetics ; Biodegradation, Environmental ; Soil/chemistry ; },
abstract = {Biochar is widely used as a soil amendment; however, information regarding its effects on soil microbial communities under tetracycline (TET) stress remains limited. In this study, metagenomic sequencing was employed to investigate the effects of TET contamination and biochar amendment on soil microbial community profiles, the abundance of antibiotic resistance genes (ARGs), and carbohydrate-active enzymes (CAZymes) genes through a pot experiment. Results showed that TET exposure reduced microbial diversity and evenness, and significantly altered the relative abundance of dominant microbes (e.g., Acidobacteriota and Candidatus_Rokubacteria) whereas biochar amendment especially at 0.5% application significantly increased both diversity and evenness, facilitated the recovery of dominant microbes, and improved community stability. TET exposure also enriched glycopeptide resistance genes and shifted CAZyme gene profiles. Overall, the metagenomic results demonstrated that reed biochar can regulate soil microbial responses under TET stress, providing insights into its role in alleviating antibiotic-induced microbial disturbance and supporting soil ecological resilience.},
}

*Charcoal/chemistry
*Soil Microbiology
*Tetracycline/pharmacology/metabolism
Metagenomics
*Bacteria/genetics/classification/drug effects/isolation & purification/metabolism
*Soil Pollutants/metabolism
*Anti-Bacterial Agents/pharmacology
*Microbiota/drug effects/genetics
Biodegradation, Environmental
Soil/chemistry

@article {pmid42801092,
year = {2026},
author = {Derrick, E and Barbosa da Costa, N and Barrett, RDH and Shapiro, BJ},
title = {Glyphosate-based herbicide exposure triggers genetic adaptation but not diversity collapse within bacterioplankton species.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag201},
pmid = {42801092},
issn = {2730-6151},
abstract = {Bacterial populations evolve rapidly in the lab when faced with experimentally applied selective pressures. Yet how bacteria evolve in nature, in more complex multi-species communities, is both challenging to study and essential to our understanding of ecosystem responses to rapid anthropogenic change. To track bacterial evolution in a semi-natural context, we applied Roundup, a glyphosate-based herbicide (GBH) that interferes with aromatic amino acid synthesis, as a selective pressure to 1000 L ponds containing bacterioplankton communities from a pristine lake. We show that both ecological and evolutionary changes can occur on short timescales after a strong selective pressure. Using metagenome-assembled genomes as a proxy for species, we found that GBH treatment substantially affected community diversity but did not purge within-species genetic diversity over the 4 weeks of the experiment. We identified several functional categories of genes consistently targeted by GBH selection across seven different species of bacteria. Genes involved in amino acid transport and metabolism were more likely to experience GBH-driven changes in allele frequency, including the gene aroA targeted by glyphosate, along with other potentially novel targets of selection. Together, these results show how environmental change can rapidly affect bacterial community structure and select for specific genetic targets without purging genetic diversity genome-wide.},
}

@article {pmid42593076,
year = {2026},
author = {Romano, ALR and Coutouné, N and Rego-Costa, A and Desai, MM and Carazzolle, MF and Gombert, AK},
title = {Dynamics of contaminant microbes in bioethanol production from sugarcane.},
journal = {Journal of industrial microbiology & biotechnology},
volume = {53},
number = {},
pages = {},
doi = {10.1093/jimb/kuag020},
pmid = {42593076},
issn = {1476-5535},
support = {2018/04962-5//FAPESP/ ; 306190/2022-2//CNPq/ ; 130582/2021-2//CNPq/ ; },
mesh = {*Saccharum/microbiology/metabolism ; *Ethanol/metabolism ; Brazil ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Fermentation ; *Biofuels ; Industrial Microbiology ; Metagenomics ; Microbiota ; },
abstract = {The dynamics and impact of microbial contaminants in industrial sugarcane bioethanol production in Brazil were investigated through a 2-year metagenomic study across two biorefineries. Shotgun metagenomic sequencing revealed that temporal shifts in the contaminant microbiome dynamics within production seasons were more pronounced than inter-annual or inter-mill variations. While Saccharomyces spp. dominated, bacterial communities, primarily within the Firmicutes phylum and dominated by the genera Lactobacillus, Limosilactobacillus, and Bacillus, exhibited dynamic changes. Correlation analyses with industrial process parameters revealed a complex interplay: lower Lactobacillus levels in one mill were associated with increased ethanol yield, whereas higher levels in another mill correlated with reduced yeast viability and increased flocculation. The presence of Limosilactobacillus was linked to decreased yeast viability, whereas Bacillus showed potential for inhibiting both Lactobacillus and Limosilactobacillus. These findings highlight the nuanced and species-specific impacts of bacterial contaminants on bioethanol production, underscoring the need for strain-level functional studies and targeted interventions to optimize fermentation efficiency and stability in industrial settings. One-Sentence Summary The dynamics of contaminant bacterial populations during fuel ethanol production from sugarcane was unrevealed in two biorefineries and in two consecutive production years using shotgun metagenomics.},
}

*Saccharum/microbiology/metabolism
*Ethanol/metabolism
Brazil
*Bacteria/classification/genetics/isolation & purification/metabolism
Fermentation
*Biofuels
Industrial Microbiology
Metagenomics
Microbiota

@article {pmid42610965,
year = {2026},
author = {Liu, ZT and Zhao, XD and Li, JQ and Li, SX and Tang, X and Zhang, SY},
title = {High molecular weight dissolved organic matter drives soil resistome proliferation by enhancing microbial competition and viral carbon metabolism.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag212},
pmid = {42610965},
issn = {1751-7370},
support = {JYB2025XDXM904//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; 22522603//National Natural Science Foundation of China/ ; 425B2046//National Natural Science Foundation of China/ ; 22522603//National Natural Science Foundation of China/ ; 425B2046//National Natural Science Foundation of China/ ; JYB2025XDXM904//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; },
mesh = {*Soil Microbiology ; *Carbon/metabolism ; Molecular Weight ; *Soil/chemistry ; *Dissolved Organic Matter/chemistry/metabolism/analysis ; *Bacteria/genetics/metabolism ; China ; *Drug Resistance, Microbial/genetics ; Metagenomics ; *Microbiota ; },
abstract = {Soil organic carbon is a key determinant of microbial community structure and function, yet the role of dissolved organic matter (DOM) bioavailability in shaping the soil antibiotic resistome remains poorly understood. Here, we combined previous continental-scale field sampling across 18 provinces in China (n = 141) with additional microcosm experiments to investigate how DOM molecular weight influences soil antibiotic resistance gene (ARG) proliferation. Using Fourier transform ion cyclotron resonance mass spectrometry and metagenomic analyses, we found that soils enriched in high molecular weight (HMW) DOM harbored significantly greater ARG abundance and diversity compared to low molecular weight DOM soils. HMW DOM intensified microbial competition, as evidenced by a higher proportion of negative correlations in the co-occurrence network and lower niche breadth, favoring the enrichment of co-hosts that simultaneously carried ARGs, carbon metabolism genes, and biosynthetic gene clusters for antimicrobial compounds. Microcosm experiments confirmed that HMW DOM (lignin) addition significantly increased ARG transcript abundance (2.4-fold) and co-host relative abundance (2.3-fold), accompanied by a concurrent increase in transcribed viral auxiliary metabolic genes (2.5-fold) involved in complex carbon degradation. Structural equation modeling revealed that HMW DOM abundance and chemodiversity exerted the strongest positive effects on ARG abundance, primarily by shaping microbial community competition and metabolic potential. Collectively, our findings establish DOM bioavailability, particularly its molecular weight, as a critical yet previously overlooked driver of soil resistome development, challenging the conventional focus on total carbon content and highlighting the potential for molecular-level organic matter management to mitigate the spread of ARGs.},
}

*Soil Microbiology
*Carbon/metabolism
Molecular Weight
*Soil/chemistry
*Dissolved Organic Matter/chemistry/metabolism/analysis
*Bacteria/genetics/metabolism
China
*Drug Resistance, Microbial/genetics
Metagenomics
*Microbiota

@article {pmid42786178,
year = {2026},
author = {Zou, X and Ni, Y and Zhang, Q and Li, S and Zhang, Y and Wang, C and Yao, X and Chang, K and Lu, B and Guo, R and Xing, G and Yu, H and Yin, J and Gan, N and Wang, Z and Yan, Q and Cao, B},
title = {OAPGC: a high-quality oral and airway prokaryotic genome catalog for enhanced ecological resolution and disease inference.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42786178},
issn = {2055-5008},
support = {2025-NHLHCRF-JBGS-B-WZ-06//National High Level Hospital Clinical Research Funding/ ; BRWEP2024W114060104//Beijing Research Ward Excellence Program/ ; XLYC2403207//Young Top Talents Program of the Liaoning Revitalization Talents Initiative/ ; ZRJY2023-GG24//China-Japan Friendship Hospital elite program/ ; 2024RJ018//Dalian Outstanding Young Scientific and Technological Talents Program/ ; 2022YFA1304303//National Key R&D Program of China/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Mouth/microbiology ; Metagenome ; *Respiratory System/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Genome, Bacterial ; Metagenomics/methods ; Phylogeny ; Case-Control Studies ; },
abstract = {The human oral cavity and airway harbor diverse microbiomes that are implicated in oral and respiratory diseases, yet comprehensive genomic catalogs remain scarce. Here, we present the Oral and Airway Prokaryotic Genome Catalog (OAPGC), comprising 99,215 high-quality, non-redundant genomes reconstructed from public and newly sequenced metagenomes and isolates. OAPGC was clustered into 2474 species using refined, phylum-specific nucleotide identity thresholds, and 29.5% of them are uncultured. Habitat-driven divergence was evident across 15 oral and 8 airway sites, with airway microbiomes showing greater inter-individual variability and enriched antibiotic resistance genes. Across 25 case-control comparisons covering 12 diseases, disease status explained significant community shifts in 19 datasets, with classifiers achieving an AUC > 0.70 in 20 datasets. Shared microbial signatures were identified for diseases such as periodontitis and pneumonia, including uncultured taxa. We also detected 12.3% of OAPGC species in the gut, whose enrichment was linked to multiple diseases and improved cross-cohort classification performance. OAPGC establishes a foundational, disease-relevant genomic framework for oral and airway microbiome studies.},
}

Humans
*Microbiota/genetics
*Mouth/microbiology
Metagenome
*Respiratory System/microbiology
*Bacteria/classification/genetics/isolation & purification
*Genome, Bacterial
Metagenomics/methods
Phylogeny
Case-Control Studies

@article {pmid42789300,
year = {2026},
author = {Li, M and Mao, J and Liu, S and Yu, H and Qin, H and Liu, X and Tu, R and Chen, S and Liu, Z and Zhang, S and Mao, J},
title = {Ethanol exposure is associated with spatial and taxon-specific gut microbiota remodeling characterized by ecological adaptation rather than broad activation of microbial ethanol metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2734657},
doi = {10.1080/19490976.2026.2734657},
pmid = {42789300},
issn = {1949-0984},
mesh = {Animals ; *Ethanol/metabolism ; Male ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Mice ; *Bacteria/classification/genetics/metabolism/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Adaptation, Physiological ; Acetaldehyde/metabolism ; Metagenomics ; },
abstract = {Alcohol-associated diseases are linked to gut microbiota disruption, but how ethanol intake is associated with microbial functional remodeling remains unclear. Here, using male C57BL/6J mice, we integrated spatiotemporal quantification of ethanol and acetaldehyde across the gastrointestinal tract with 16S rRNA sequencing, metagenomics, metaproteomics, and metabolomics. Our results showed that small-intestinal communities were enriched in taxa and functions related to bile acid tolerance/utilization, whereas cecal communities exhibited pronounced remodeling of multiple core functions associated with ecological adaptation. Although the abundance of several ethanol metabolism-related genes increased, this genetic potential was not broadly translated into detectable protein-level activation. Ethanol metabolism-related proteins were mainly derived from Lachnospiraceae, whose metabolic activity was suppressed. In contrast, Muribaculaceae, Desulfovibrionaceae, and Barnesiellaceae gained functional advantages in substrate acquisition, energy metabolism, oxidative stress defense, and proteostasis. These findings provide a region-resolved functional map indicating that ethanol-associated microbiota remodeling is characterized by ecological adaptation, rather than uniform activation of direct microbial ethanol metabolism.},
}

Animals
*Ethanol/metabolism
Male
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
Mice
*Bacteria/classification/genetics/metabolism/isolation & purification/drug effects
RNA, Ribosomal, 16S/genetics
Adaptation, Physiological
Acetaldehyde/metabolism
Metagenomics

@article {pmid42792947,
year = {2026},
author = {Du, Q and Xing, L and Zhu, C and Li, P},
title = {Gut Microbiota and Metabolic Pathway Signatures for Inflammatory Bowel Disease Identified via Subject-Stratified Random Forest Based on the Longitudinal HMP2 Cohort.},
journal = {Genes},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/genes17091053},
pmid = {42792947},
issn = {2073-4425},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Random Forest ; *Metabolic Networks and Pathways/genetics ; *Gastrointestinal Microbiome/genetics ; Longitudinal Studies ; Feces/microbiology ; Female ; Machine Learning ; },
abstract = {Background: Inflammatory bowel disease (IBD) is characterised by severe intestinal microbial dysbiosis. Most machine learning diagnostic models built on the longitudinal HMP2 cohort suffer serious data leakage from random sample-level cross-validation splitting, which leads to artificially inflated AUC values. Additionally, incomplete reporting of microbial preprocessing, random forest hyperparameters and multi-dimensional evaluation metrics reduces the reproducibility of existing research. Methods: We re-analysed the public HMP2 (IBDMDB) longitudinal metagenomic dataset containing 130 unique subjects (103 IBD/27 healthy controls) and 1627 longitudinal faecal samples. Raw 585 species were filtered by a minimum relative abundance of 1 × 10[-5] and sample prevalence ≥20%, retaining 89 taxa; all 1135 metabolic pathways were retained. CLR transformation was applied to compositional abundance data. We performed Wilcoxon differential testing with Benjamini-Hochberg FDR correction, alpha/beta diversity analysis, and three random forest models (filtered species, all FDR-significant pathways, strictly filtered pathways). Critical improvements included subject-ID-stratified 5-fold cross-validation repeated 5 times, within-fold training-set-only feature importance calculation, and class weighting to balance unbalanced IBD/control samples. PERMANOVA with subject stratification and PERMDISP dispersion test were implemented with 999 fixed-seed permutations. Results: All four alpha diversity indices were significantly lower in IBD patients (all p < 0.0001). Subject-stratified PERMANOVA showed disease status only explained 1.18% of total Bray-Curtis community variance (R[2] = 0.0118, p = 1); PERMDISP detected significant group dispersion heterogeneity (p = 0.027). We identified 63 differentially abundant species and 695 perturbed pathways at FDR < 0.05. Canonical butyrate producers Faecalibacterium prausnitzii and Roseburia hominis showed no significant inter-group differences. Bootstrap 1000-resampling AUC 95% CIs indicated moderate classification performance: species model (0.626-0.705, mean AUC = 0.665), all-significant-pathway model (0.645-0.712, mean AUC = 0.679), strict-pathway model (0.620-0.685, mean AUC = 0.654). Alistipes putredinis and peptidoglycan biosynthesis I were the top taxonomic and pathway biomarkers, respectively. Conclusions: This study established a leakage-free machine learning pipeline for longitudinal microbiome cohorts via subject-level cross-validation splitting. The moderate AUC values eliminate false high performance caused by sample leakage, and we provide reliable candidate microbial and metabolic biomarkers for IBD. Restricted by single-cohort internal validation and unadjusted medication confounders, these markers still require independent multi-centre external verification before clinical translation.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/metabolism/genetics
Random Forest
*Metabolic Networks and Pathways/genetics
*Gastrointestinal Microbiome/genetics
Longitudinal Studies
Feces/microbiology
Female
Machine Learning

@article {pmid42794458,
year = {2026},
author = {Carini, F and Sorce, A and Ciuppa, ME and David, S and Giammanco, M and Di Carlo, P and Evola, S and Tomasello, G and Mulè, G and Carollo, C},
title = {Gut, Oral, and Fungal Microbiota in Hypertension: A Multi-Compartment Systematic Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188029},
pmid = {42794458},
issn = {1422-0067},
mesh = {Humans ; *Hypertension/microbiology ; *Mouth/microbiology ; *Gastrointestinal Microbiome ; *Mycobiome ; *Microbiota ; *Fungi ; },
abstract = {The gut microbiota is an established modulator of blood pressure, but the oral bacteriome and the fungal mycobiome have been examined largely in isolation from it and from each other. No previous synthesis has evaluated all three compartments within one analytical framework, or treated sex and ethnicity as primary analytical axes rather than adjustment covariates. Systematic review reported according to PRISMA 2020 and, for the synthesis, the SWiM guideline. PubMed/MEDLINE, Embase, Scopus, and Web of Science were searched from inception to 30 June 2026. Observational human studies in adults reporting gut, oral, or fungal microbiota data stratified by blood pressure status were eligible, together with Mendelian randomisation studies and studies with a nested experimental causal component. Two reviewers screened and extracted independently, with a third resolving disagreement. Risk of bias was assessed with the Newcastle-Ottawa Scale and certainty of evidence with GRADE adapted for exposure-outcome questions. Increased abundance of the Ruminococcus gnavus group was the most convergent taxon-level finding, replicated in three independent populations on two continents, including one prospective multi-ethnic cohort with full adjustment and correction for multiple comparisons (OR 1.07, 95% CI 1.01-1.14 for incident hypertension). In the oral compartment, depletion of the nitrate-reducing commensal Neisseria subflava converged across a United States prospective cohort and an Italian case-control study using unrelated methods, and salivary nitric oxide was approximately three-fold lower in hypertensive subjects. Depletion of the short-chain fatty acid producers Faecalibacterium and Roseburia and enrichment of Klebsiella were convergent but geographically restricted. Mycobiome evidence was contradictory: two studies reported fungal dysbiosis, one of them already at the pre-hypertensive stage, while a cross-cohort metagenome-wide study on two independent cohorts from Beijing and Dalian (N = 159 hypertensive patients, 101 healthy controls) identified 61 gut bacterial species with consistent altered abundance across both cohorts while finding no replicable mycobiome signal. Recurring across compartments and kingdoms was the collapse of microbial co-correlation networks in hypertension, alongside a dissociation between null alpha diversity and significant beta diversity. Associations differed by ethnicity within a single multi-ethnic cohort and were generally stronger in women. Certainty of evidence, assessed per individual convergent finding, was very low for every taxon-level finding and low for salivary nitric oxide; these ratings concern the attribution of hypertension to specific organisms, not the existence of a microbiota-hypertension association, which is supported at community level in every compartment examined and by experimental transfer models. That the microbiota differs in hypertension is well supported; which organisms are responsible is not. The most reproducible signal is structural rather than taxonomic, and conventional differential-abundance analysis is not designed to detect it. No individual microbial taxon is currently ready to serve as a marker of hypertension or to inform clinical practice.},
}

Humans
*Hypertension/microbiology
*Mouth/microbiology
*Gastrointestinal Microbiome
*Mycobiome
*Microbiota
*Fungi

@article {pmid42794824,
year = {2026},
author = {Kim, M and Song, WH and Ju, HJ and Koh, YK and Kim, SJ and Lee, YB and Lee, M},
title = {Shotgun Metagenomic Characterization of Skin Microbiome Shifts in Human Scabies Before and After Scabicidal Treatment.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188397},
pmid = {42794824},
issn = {1422-0067},
mesh = {Humans ; *Scabies/drug therapy/microbiology ; *Skin Microbiome ; *Metagenomics/methods ; Male ; Female ; *Skin/microbiology ; Shotgun Sequencing ; Sarcoptes scabiei ; Metagenome ; Adult ; *Microbiota ; },
abstract = {Scabies, caused by Sarcoptes scabiei, is a globally prevalent ectoparasitic infestation associated with intense pruritus and secondary bacterial infection, yet the molecular composition of the skin microbiome during active infestation remains poorly characterized. We performed shotgun metagenomic sequencing of 41 skin samples collected from 18 patients at dry and moist anatomical sites before and after scabicidal treatment. In exploratory group-level comparisons, pretreatment moist-site samples had lower alpha diversity and higher bacterial and viral read-based burdens than post-treatment moist-site samples. Pretreatment dry and moist samples did not differ significantly in diversity, and Staphylococcus was the predominant genus. No genus- or species-level taxon or predicted pathway remained statistically significant after Benjamini-Hochberg false discovery rate correction at a threshold of 0.05. Nominal differences in predicted purine biosynthesis pathways were interpreted as exploratory observations. These findings provide a shotgun metagenomic characterization of the skin microbiome during active scabies and describe exploratory treatment-associated patterns that require confirmation in larger, paired longitudinal studies.},
}

Humans
*Scabies/drug therapy/microbiology
*Skin Microbiome
*Metagenomics/methods
Male
Female
*Skin/microbiology
Shotgun Sequencing
Sarcoptes scabiei
Metagenome
Adult
*Microbiota

@article {pmid42795487,
year = {2026},
author = {Che, M and Zhang, J and Kudelaiti, K and Zhang, J and Liusui, Y and Dong, Z},
title = {Effects of Co-Application of γ-Polyglutamic Acid and Chemical Fertilizer on Rhizosphere Microbial Community Structure and Function of Cotton at Different Growth Stages in an Arid Cotton Field.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091905},
pmid = {42795487},
issn = {2076-2607},
support = {2024D01A82//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
abstract = {Long-term excessive nitrogen application in arid cotton fields increases nitrate leaching risk during fallow and disrupts rhizosphere microecology. To clarify the cross-growth-stage regulatory effects of the biostimulant γ-polyglutamic acid (γ-PGA) combined with chemical fertilizer on rhizosphere microbial communities, we compared chemical fertilizer alone (NK) and γ-PGA plus chemical fertilizer (GT) using rhizosphere soils collected at boll-setting (August) and fallow (October), with physicochemical measurements and metagenomic sequencing technology. At boll-setting, GT lowered pH by 0.74 units compared with NK and increased NH4[+]-N, NO3[-]-N, and TN by 339.3%, 491.4%, and 23.0%, respectively. By fallow, GT increased TOC by 70.6% and maintained NH4[+]-N at 18.38 mg/kg, while NK accumulated 66.85 mg/kg NO3[-]-N. GT buffered post-harvest fungal community disturbance (Shannon: GT 4.06 vs. NK 2.80) and shifted bacterial communities toward oligotrophic taxa and archaea toward ammonium-preferring taxa. A metagenomic LEfSe analysis showed that GT was enriched in functional genes related to [Q]: Secondary metabolite biosynthesis, transport and catabolism, [T]: Signal transduction mechanisms, and [V]: Defense mechanisms, indicating a shift from resource acquisition to conservative maintenance. Mantel tests revealed that microbial functional profiles showed the strongest association with NH4[+]-N (r = 0.828 in August, r = 0.883 in October, p < 0.001). Thus, γ-PGA with chemical fertilizer stabilizes fallow rhizosphere microbial communities, reduces nutrient leaching, and promotes carbon-nitrogen co-retention.},
}

@article {pmid42795606,
year = {2026},
author = {Méndez-Rodríguez, A and Ledesma, J and López-González, C and Zarza, H and López-Wilchis, R and Labiod, N and Cuesta, I and Casas, I and Echevarría, JE and Vázquez, A and Juste, J},
title = {Virome Diversity in Three Bat Species in Different Environments in Southern Spain.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092025},
pmid = {42795606},
issn = {2076-2607},
support = {PLEC2021-007968//NEXTHREAT/ ; //European Union NextGeneration EU/PRTR funds/ ; },
abstract = {Viruses represent a major component of global biodiversity and are integral to ecological and evolutionary processes shaping host populations and communities. Bats, with high species richness and ecological diversity, provide a system to examine how host traits and environmental context structure viral communities. Here, we characterize viral diversity from three bat species (Pipistrellus kuhlii, Cnephaeus isabellinus, and Nyctalus lasiopterus) using samples across two environments in southern Spain: a well-preserved Mediterranean forest (Sierras de Cazorla, Segura, and Las Villas Natural Park, CSVNP) and a human-modified wetland-agrosystem mosaic (Doñana National Park, DNP). Metagenomics detected 72 eukaryotic virus species, including viruses reported in mammals, insects, arachnids, and plants. Viral richness and composition varied among samples, bat species, and environments. Samples of P. kuhlii exhibited the highest richness, driven by insect-associated viruses. C. isabellinus showed a higher contribution of vertebrate-related viruses, whereas N. lasiopterus exhibited the lowest richness. CSVNP samples showed higher viral richness and more exclusive taxa, whereas DNP samples exhibited lower richness, with a greater contribution of arthropod-associated viruses, potentially reflecting prey communities. Despite this, diversity metrics were similar between environments, indicating structurally comparable communities composed of distinct taxa. Bat viromes appear to be associated with host ecology, trophic behavior, and environmental context.},
}

@article {pmid42796698,
year = {2026},
author = {Huang, J and Zhao, H and Wang, F and Zeng, B and Ma, Z and Wang, R and Yang, Y and Amier, M and Yilihaer, B and Lu, Y},
title = {Whole-Genome Sequencing and Intestinal Metagenome Sequencing Revealed the Carriage and Transmission of Salmonella enterica in Xinjiang, China.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/pathogens15090930},
pmid = {42796698},
issn = {2076-0817},
mesh = {*Salmonella enterica/genetics/isolation & purification/classification ; Humans ; China/epidemiology ; Whole Genome Sequencing ; *Salmonella Infections/transmission/microbiology/epidemiology ; *Metagenome ; Phylogeny ; *Gastrointestinal Microbiome ; Feces/microbiology ; Virulence Factors/genetics ; *Carrier State/microbiology/epidemiology ; Metagenomics ; Genome, Bacterial ; },
abstract = {Background:Salmonella enterica, a major foodborne pathogen, poses a severe global public health threat. However, data regarding its carriage characteristics, transmission patterns, and association with intestinal microbiota in healthy populations of Xinjiang, China, remain insufficient, limiting the formulation of targeted salmonellosis prevention and control strategies. Methods: In this study, 31 Salmonella enterica strains isolated from more than 2000 healthy individuals in Urumqi were subjected to whole-genome sequencing to analyze serovars, antimicrobial resistance (AMR) genes, and virulence genes. Meanwhile, metagenomic sequencing was performed on 50 fecal samples (culture negative) from 2000 healthy individuals to investigate intestinal microbiota structure, Salmonella enterica prevalence, and related microbial taxa. Results: The results showed that 60% of samples (30/50) were positive by the read-based criterion (≥1000 Salmonella-specific reads), while the assembly-verified criterion (≥1000 reads and contigs > 1 kb) confirmed Salmonella-specific sequences in 12% (6/50). Among the 31 culture-confirmed isolates, Salmonella Typhimurium and Salmonella Paratyphi B were the dominant serovars, together accounting for 60%. All isolates harbored core virulence genes for Type III secretion system and adhesion factors, with low AMR gene carriage and no multidrug-resistant strains. Phylogenetic analysis showed that Urumqi-derived isolates were distributed across multiple genomic clusters, suggesting active inter-regional circulation of S. enterica within the available dataset. Salmonella enterica carriage did not affect gut microbial α-diversity but altered community composition, with Escherichia coli, Shigella flexneri, and Klebsiella pneumoniae as key associated taxa. Conclusions: This study found that Urumqi-derived isolates are widely distributed across genomic clusters in Xinjiang, with a unique local transmission chain identified, though definitive source attribution requires further geographically balanced sampling. Salmonella enterica carriage exhibited ecological niche synergy with intestinal Enterobacteriaceae, but did not significantly affect gut microbial diversity.},
}

*Salmonella enterica/genetics/isolation & purification/classification
Humans
China/epidemiology
Whole Genome Sequencing
*Salmonella Infections/transmission/microbiology/epidemiology
*Metagenome
Phylogeny
*Gastrointestinal Microbiome
Feces/microbiology
Virulence Factors/genetics
*Carrier State/microbiology/epidemiology
Metagenomics
Genome, Bacterial

@article {pmid42797815,
year = {2026},
author = {Moreira, G and Silva, E and Mourão, J and Mesquita, JR},
title = {First European Identification of a Partial Tacheng Tick Virus 8-like Underscores the Hidden Burden of Tick-Borne Flavivirus-like Viruses.},
journal = {Viruses},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/v18090984},
pmid = {42797815},
issn = {1999-4915},
support = {2025.05151.BD//Fundação para a Ciência e Tecnologia/ ; },
mesh = {Animals ; Phylogeny ; Genome, Viral ; *Flavivirus/genetics/classification/isolation & purification ; Portugal ; Dermacentor/virology ; *Ticks/virology ; },
abstract = {Tick-associated viruses are an underexplored component of global viromes, and highly divergent RNA viruses often remain undetected due to low abundance and sequence divergence. Tacheng tick virus 8 (TcTV8) is a poorly characterized RNA flavivirus-like virus originally reported from Dermacentor-associated ticks in China, with few subsequent reports and no confirmed detections outside Asia. Here, we report the detection and partial genomic characterization of a TcTV8-like virus in ticks collected from Portugal. Sequence-independent (SISPA) nanopore sequencing of individual ticks recovered three partial fragments (~2.7 kb, ~14% of the reference genome; ~30% of the reference covered at ≥1×), which shared high amino-acid identity with the TcTV8 polyprotein, including a methyltransferase-region domain. Phylogenetic analysis placed the Portuguese sequence within the TcTV8 lineage. Read-level classification and coverage analysis further support the presence of this virus in the positive sample. These findings represent, to our knowledge, the first detection of a TcTV8-like virus in European ticks, extending its known geographic range beyond Asia. The detection of this cryptic viral lineage highlights the need for broader tick virome surveillance to better understand the diversity, evolution, and ecology of flavivirus-like viruses.},
}

Animals
Phylogeny
Genome, Viral
*Flavivirus/genetics/classification/isolation & purification
Portugal
Dermacentor/virology
*Ticks/virology

@article {pmid42797867,
year = {2026},
author = {Kushugulova, A and Kamzayeva, N and Kozhakhmetov, S and Vinogradova, E and Jarmukhanov, Z and Mukhanbetzhanov, N and Kovenskiy, A and Kossumov, A and Rakhmankulova, A and Ukybassova, T},
title = {Cervicovaginal Virome Restructuring Associated with HPV Status, Bacterial Dysbiosis, and Cervical Cytological Abnormalities.},
journal = {Viruses},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/v18091036},
pmid = {42797867},
issn = {1999-4915},
support = {BR24992853//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Humans ; Female ; *Human Papillomavirus Viruses/genetics/isolation & purification/classification ; *Cervix Uteri/virology/pathology/microbiology ; *Vagina/virology/microbiology ; *Papillomavirus Infections/virology ; *Dysbiosis/virology/microbiology ; *Virome ; Bacteria/classification/genetics ; Bacteriophages/genetics ; Microbiota ; Metagenomics ; Papillomaviridae/genetics ; },
abstract = {The cervicovaginal virome remains poorly characterized in relation to human papillomavirus (HPV) infection and bacterial community structure. We performed shotgun metagenomic sequencing of 311 cervicovaginal specimens from a Kazakhstani cohort spanning seven groups defined by HPV status and cervical cytology. Viral community composition differed according to HPV status, with increasing representation of the oncogenic Alphapapillomavirus 9 clade across more abnormal cytological categories. Predicted phage functional profiles also differed between NILM HPV-positive and NILM HPV-negative women. Integrase, excisionase, transcriptional repressor, anti-repressor Ant, and amidase annotations showed differential prevalence after false-discovery-rate correction. Auxiliary metabolic and host-interaction genes associated with nucleotide metabolism, DNA modification, anti-restriction functions, and toxin-antitoxin systems were also differentially represented. Stratification by bacterial community state type revealed contrasting predicted functional repertoires, with toxin-antitoxin-associated annotations enriched in Lactobacillus crispatus-dominated communities and anti-restriction-associated annotations enriched in Gardnerella vaginalis-dominated communities. These findings identify associations between HPV status, bacterial community structure, and cervicovaginal viral composition and predicted phage functions. Longitudinal and experimental studies are required to determine the directionality and biological activity of these associations.},
}

Humans
Female
*Human Papillomavirus Viruses/genetics/isolation & purification/classification
*Cervix Uteri/virology/pathology/microbiology
*Vagina/virology/microbiology
*Papillomavirus Infections/virology
*Dysbiosis/virology/microbiology
*Virome
Bacteria/classification/genetics
Bacteriophages/genetics
Microbiota
Metagenomics
Papillomaviridae/genetics

@article {pmid42798402,
year = {2026},
author = {Ahn, J and Kim, M and Min, SH and Bae, HG and Bae, JY and Kwon, J and Yi, H and Park, DH},
title = {Fecal microbiota transplantation from duodenal light stimulation-conditioned donors is associated with improved glucose tolerance and intestinal incretin-related remodeling in diabetic Goto-Kakizaki rats.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1900693},
pmid = {42798402},
issn = {2235-2988},
mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; Rats ; *Diabetes Mellitus, Type 2/therapy/metabolism ; *Incretins/metabolism ; *Gastrointestinal Microbiome ; *Duodenum/microbiology ; Male ; Glucose Tolerance Test ; Disease Models, Animal ; Blood Glucose ; Feces/microbiology ; },
abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) is a complex metabolic disorder characterized by impaired glucose homeostasis and β-cell dysfunction. Emerging evidence suggests that the gut microbiota-incretin axis may contribute to metabolic regulation. However, whether microbiota from duodenal light stimulation (DLS)-conditioned donors can influence metabolic phenotypes via fecal microbiota transplantation (FMT) remains unclear.

METHODS: We evaluated whether FMT from DLS-conditioned donors was associated with metabolic and intestinal changes in diabetic GK (Goto-Kakizaki) rats. Recipients received FMT from week -2 to week 0 and were then followed for 7 weeks after the final FMT dose. Metabolic phenotyping, intestinal histology, short-chain fatty acid (SCFA) profiling, and shotgun metagenomic profiling of bacterial and viral communities were performed.

RESULTS: FMT recipients showed within-group improvement in OGTT glucose profiles, without significant changes in fasting glucose levels. Total glucose AUC0-120 was significantly reduced within the FMT group in the within-group (period) comparison; however, the group × period interaction was not significant, indicating no statistically significant longitudinal between-group treatment effect. Early GLP-1 responses showed a modest increasing trend in FMT recipients, whereas total GLP-1 AUC0-120 was not significantly changed. HOMA-β (homeostatic model assessment of β-cell function) increased within the FMT group, and pancreatic insulin-positive area was greater in FMT recipients than in controls at the study endpoint. Intestinal remodeling was evident, including an increased villus:crypt ratio and increased colonic GLP-1-positive cells. FMT was associated with fecal bacteriome differences, including one FDR-significant taxon and several nominally associated taxa, such as Akkermansia muciniphila and Xylanibacter rodentium. No significant global shift in fecal virome composition was observed, although selected viral taxa showed nominal group-associated differences that did not remain significant after FDR correction. Exploratory network analysis suggested group-specific bacteriome-virome association patterns after FMT.

CONCLUSION: FMT from DLS-conditioned donors was associated with improved glucose tolerance, intestinal incretin-related remodeling, increased pancreatic insulin-positive area, and fecal bacteriome differences in diabetic GK rats based on within-group longitudinal changes for the glucose- and β-cell-related outcomes, for which the group × period interactions were not significant, whereas the histological and microbiome differences reflect cross-sectional between-group comparisons at the study endpoint. These findings support a hypothesis-generating link between donor-conditioned FMT, intestinal remodeling, and microbiome-associated metabolic regulation, while further studies are required to define DLS-specific and donor-derived effects.},
}

Animals
*Fecal Microbiota Transplantation/methods
Rats
*Diabetes Mellitus, Type 2/therapy/metabolism
*Incretins/metabolism
*Gastrointestinal Microbiome
*Duodenum/microbiology
Male
Glucose Tolerance Test
Disease Models, Animal
Blood Glucose
Feces/microbiology

@article {pmid42798947,
year = {2026},
author = {Yin, Y and Ma, Y and Wang, Y and Gao, P and Jia, C and Li, C and Yang, Q and Zhang, F and Bo, H and Wang, R and Chen, J},
title = {Chemical heterogeneity and mixed pollution are associated with microbial functional potential across soils in a coal mining subsidence landscape.},
journal = {RSC advances},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6ra03694e},
pmid = {42798947},
issn = {2046-2069},
abstract = {Coal mining subsidence occurs when underground coal extraction removes structural support for overlying strata, causing ground deformation and localized surface collapse. However, it remains unclear whether soils across a subsidence landscape respond in a similar way, or whether different habitats develop distinct nutrient conditions and mixtures of heavy metals and PAHs that are associated with different microbial communities and carbon, nitrogen, and sulfur cycling potentials. Local ecological risks would be overlooked if the entire subsidence zone is generalized as one disturbed ecosystem. Here, we sampled surface soils (0-20 cm) in September 2024 from four ordered habitats along a local subsidence associated topographic habitat in Jining, China: subsidence soil (SS), ditch soil adjacent to the subsidence area (SL), ditch soil near farmland (SR), and farmland soil (SF). We quantified soil physicochemical properties, heavy metals, polycyclic aromatic hydrocarbons (PAHs), and enzyme activities, and characterized bacterial and fungal communities and functional genes using metagenomic sequencing and downstream multivariate analyses. Soil chemical conditions differed consistently across habitats, with clear separation along nutrient related gradients and distinct contaminant profiles among habitats. Microbial α-diversity and β-diversity showed specific habitat patterns, and community composition differed among habitats for both bacteria and fungi. Functional profiles related to carbon, nitrogen, and sulfur cycling also varied across habitats, indicating that chemical heterogeneity and mixed pollution coincided with reconfiguration of microbial metabolic potential at the pathway and gene levels. Ordination analyses further showed that microbial community structure and functional potential were strongly associated with soil physicochemical gradients and pollutant variables, while enzyme activities covaried with key soil properties and contaminants. Our results indicate that coal mining subsidence landscapes contain multiple habitat-specific chemical and contaminant filters rather than a single uniform "subsidence effect", supporting chemically informed, habitat-stratified assessment of soil condition and microbial functional potential in mining-affected ecosystems.},
}

@article {pmid42379362,
year = {2026},
author = {Piantoni, P and Sardi, MI and Aumiller, T and Khafipour, E and Roman-Garcia, Y and Chakrabarti, A and Dieho, K and Aubert, T and Schroeder, GF},
title = {Effects of increasing doses of a phytogenic product based on condensed tannins and spices on production performance and rumen microbiome of lactating dairy cows fed a low-protein diet.},
journal = {Journal of dairy science},
volume = {109},
number = {10},
pages = {10489-10505},
doi = {10.3168/jds.2025-28174},
pmid = {42379362},
issn = {1525-3198},
mesh = {Animals ; Female ; *Rumen/microbiology ; Cattle/physiology/microbiology ; *Lactation/drug effects ; Diet/veterinary ; *Proanthocyanidins/administration & dosage/metabolism ; Animal Feed/analysis ; *Spices/analysis ; Milk/chemistry/metabolism ; *Microbiota/drug effects ; Dietary Proteins/metabolism ; Animal Nutritional Physiological Phenomena ; Dose-Response Relationship, Drug ; },
abstract = {The objective of this experiment was to determine the effect of increasing doses of a phytogenic product based on condensed tannins and spices (CTS) on production performance of lactating dairy cows fed a low-protein diet. Eight rumen-cannulated Holstein Friesian dairy cows (140 ± 86 DIM; 39.0 ± 5 kg/d milk yield; mean ± SD) were used in a replicated 4 × 4 Latin square design experiment with 4-wk periods. Treatments were 0, 10, 20, and 30 g/d CTS (CTR, 10CTS, 20CTS, and 30CTS, respectively). The grass- and corn silage-based diet was 55.2% forage, 38.7% NDF, 21.0% total starch, and 14.6% CP. Orthogonal contrasts were used to evaluate the linear and quadratic effect of increasing doses of CTS. Results follow the order CTR, 10CTS, 20CTS, and 30CTS. Increasing doses of CTS quadratically increased DMI (25.4, 25.9, 26.1, and 25.1 kg/d) and milk yield (37.1, 38.5, 37.7, and 36.3 kg/d), tended to increase fat- and protein-corrected milk (36.9, 37.6, 37.4, and 36.1 kg/d), and did not affect feed or N efficiency (1.45% ± 0.2% and 32.0% ± 2.3%, respectively). Treatments did not affect milk fat yield (1.48 ± 0.2 kg/d) but increasing doses of CTS increased milk protein yield quadratically (1.22, 1.27, 1.26, and 1.20 kg/d). Intermediate doses of CTS tended to increase de novo fatty acid yield (352, 369, 373, and 356 g/d) and decrease trans-10 C18:1 (4.31, 4.05, 4.05, and 4.24 g/d) compared with CTR and 30CTS. Treatments did not affect milk urea concentration (17.8 ± 1.7 mg/dL) or milk CP (3.39% ± 0.2%) or fat (4.06% ± 0.2%) content. Rumen pH and time below rumen pH of 5.8 were not affected by level of CTS supplementation. A treatment by time interaction for rumen ammonia concentration indicated that 20CTS and 30CTS increased ammonia concentration 3 h after feeding compared with CTR and 10CTS (7.72, 7.94, 13.7, and 14.1 mg/dL). The 10CTS treatment decreased rumen propionate concentration only at 3 h after feeding compared with the other treatments. Apparent DM and NDF total-tract digestibility were not affected by treatments. Shotgun metagenomics were used to evaluate the effect of CTS supplementation on the solid- and liquid-associated rumen microbiome. Treatment effects were only observed in the solid-associated microbiome. Supplementation of CTS linearly decreased α diversity at both the taxa and functional levels, indicating promotion of a leaner microbial community with higher doses of CTS. Differential abundance analysis identified 26 species with large fold changes, including some species with a high presence of cellulases and significant correlations with phenotypic parameters such as DMI, N efficiency, and milk production. In conclusion, a mixture of CTS affected microbiome and rumen metabolism, increasing fat- and protein-corrected milk yield when fed at 10 and 20 g/d only. This experiment demonstrates the importance of in vivo dose-response experiments with phytogenic products to determine optimum dosage for improved rumen metabolism and performance.},
}

Animals
Female
*Rumen/microbiology
Cattle/physiology/microbiology
*Lactation/drug effects
Diet/veterinary
*Proanthocyanidins/administration & dosage/metabolism
Animal Feed/analysis
*Spices/analysis
Milk/chemistry/metabolism
*Microbiota/drug effects
Dietary Proteins/metabolism
Animal Nutritional Physiological Phenomena
Dose-Response Relationship, Drug

@article {pmid42442424,
year = {2026},
author = {Luo, Z and Zhang, K and Wang, L and Zhang, J and Huang, Y and Lu, X and Zhao, F and Cao, S and Li, J},
title = {Astragalus polysaccharides reshape gut resistome of postpartum dairy cows.},
journal = {Bioresource technology},
volume = {461},
number = {},
pages = {135399},
doi = {10.1016/j.biortech.2026.135399},
pmid = {42442424},
issn = {1873-2976},
mesh = {Animals ; *Polysaccharides/pharmacology ; Cattle ; *Astragalus Plant/chemistry ; Female ; *Postpartum Period ; Feces/microbiology ; Metagenome ; *Gastrointestinal Microbiome/drug effects/genetics ; Dairying ; Virulence Factors/genetics ; *Drug Resistance, Microbial/genetics/drug effects ; Genes, Bacterial ; },
abstract = {Antibiotic resistance genes (ARGs) in livestock feces represent an important environmental reservoir of antimicrobial resistance. Natural product intervention is a potential strategy for regulating the gut microbiome of livestock; however, its effects on the gut resistome of postpartum dairy cows remain poorly understood. In this study, we investigated the effects of Astragalus polysaccharides (APS) supplementation on the fecal microbiome, ARGs, mobile genetic elements (MGEs), virulence factors (VFs), and ARG-carrying metagenome-assembled genomes (MAGs) in dairy cows during postpartum period. Alpha and beta diversity analyses showed that APS supplementation did not significantly alter the global resistome, mobilome, or virulome structure. The content of several ARGs and VFs, including AAC(6')-Iw, qacEdelta1, ast, PM_RS00425, and sdrF, significantly decreased in the APS group, and several plasmid-associated MGEs genes showed group-specific changes. Co-occurrence network analysis revealed complex associations between ARGs, VFs, and core bacterial taxa, with Paludibacter and Parabacteroides identified as potential microbial reservoirs of resistance- and virulence-associated genes. Furthermore, 101 metagenome-assembled genomes (MAGs) were recovered, 42 of which carried multiple ARGs. Bin.1, assigned to Scatovivens, had the highest ARG count. APS supplementation reduced the overall ARG load, particularly the ARG contribution in bin.1. However, APS utilization potential was not significantly correlated with ARG density or ARG load across MAGs. Thus, this study provides new insights into APS supplementation and nutritional strategies that can mitigate the fecal ARG burden in dairy production.},
}

Animals
*Polysaccharides/pharmacology
Cattle
*Astragalus Plant/chemistry
Female
*Postpartum Period
Feces/microbiology
Metagenome
*Gastrointestinal Microbiome/drug effects/genetics
Dairying
Virulence Factors/genetics
*Drug Resistance, Microbial/genetics/drug effects
Genes, Bacterial

@article {pmid42462831,
year = {2026},
author = {Qiang, H and Jing, Y and Xu, X and Heo, S and Liu, Z and Yue, X and Zhou, A and Fernández-Morales, FJ and Oleskowicz-Popiel, P},
title = {N-(3-oxohexanoyl)-homoserine lactone-assisted enrichment reshapes functional microbial consortia for chain elongation in electrofermentation.},
journal = {Bioresource technology},
volume = {461},
number = {},
pages = {135425},
doi = {10.1016/j.biortech.2026.135425},
pmid = {42462831},
issn = {1873-2976},
mesh = {*Fermentation/drug effects ; *4-Butyrolactone/analogs & derivatives/metabolism/pharmacology ; *Microbial Consortia/drug effects/physiology ; Bacteria/metabolism ; Caproates/metabolism ; Sewage/microbiology ; },
abstract = {The functional microbial consortia supporting chain elongation determine medium-chain carboxylate recovery from organic wastes, but how signal-molecule-assisted enrichment shapes chain-elongating bacteria (CEB), electroactive bacteria (EAB), and competing guilds in electrofermentation remains unclear. Here, three N-acyl-homoserine lactones: N-butyryl-homoserine lactone (C4-HSL), N-octanoyl-homoserine lactone (C8-HSL), and N-(3-oxohexanoyl)-homoserine lactone (3OC6-HSL), were supplied during microbial enrichment, and the subsequent electrofermentation was conducted fed with sludge fermentation broth. Compared with the Control (without signaling molecules), 3OC6-HSL had the strongest response, increasing caproate production by 94.0%, compared with 16.9% and 27.3% for C4-HSL and C8-HSL, respectively. It also increased the apparent caproate electron transfer efficiency by 20.7 percentage points, increased the abundance of CEB (44.9% vs. 33.2%) and EAB (14.3% vs. 6.6%), and reduced the abundance of homoacetogens (12.1% vs. 33.7%). Co-occurrence network analysis revealed more modular and compact inferred associations, with 25.0% more modules and a 34.7-49.3% shorter average path length. Metagenomic analysis revealed enhanced reverse β-oxidation, QS, chemotaxis, and flagellar assembly potentials, and the expression levels of acetyl-CoA acyltransferase (ACAT/fadA) and acyl-CoA dehydrogenase (ACADS/ACADM) increased by 162.1% and 96.6%, respectively. Clostridium kluyveri dominated the ACAT contribution (85.9%). Overall, enrichment-phase 3OC6-HSL supplementation was associated with a caproate-oriented microbial consortium and improved caproate recovery without continuous signal dosing.},
}

*Fermentation/drug effects
*4-Butyrolactone/analogs & derivatives/metabolism/pharmacology
*Microbial Consortia/drug effects/physiology
Bacteria/metabolism
Caproates/metabolism
Sewage/microbiology

@article {pmid42468699,
year = {2026},
author = {Qing, C and Zhou, Y and Wang, Y and Li, P and Hedlund, B},
title = {Arsenic detoxification mediated by mutualistic cross-feeding in a thermophilic microbial consortium.},
journal = {Bioresource technology},
volume = {461},
number = {},
pages = {135440},
doi = {10.1016/j.biortech.2026.135440},
pmid = {42468699},
issn = {1873-2976},
mesh = {*Arsenic/metabolism/toxicity ; *Microbial Consortia/physiology ; Biodegradation, Environmental ; Photosynthesis ; *Cyanobacteria/metabolism ; Hot Springs/microbiology ; *Symbiosis ; Inactivation, Metabolic ; Oxidation-Reduction ; Coculture Techniques ; },
abstract = {Cyanobacteria-dominated microbial mats thrive in arsenic (As)-rich hot springs, but how they cope with As stress remains unclear. This study explored the As detoxification strategy of a photosynthetic microbial mat from a high-As hot spring in Tibet. The photosynthetic mat oxidized arsenite [As(Ⅲ)] under light without external organic carbon sources or electron acceptors. However, As(Ⅲ) was not oxidized by a pure culture of the dominant cyanobacterium isolated from the mat, "Thermoleptolyngbya sichuanensis" XZ-Cy5. Instead, exposure of a growing culture to 5 mM As(Ⅲ) led to rapid loss of chlorophyll and photosynthetic activity. In contrast, a pure culture of the mat-derived heterotroph Chelatococcus sp. XZ-Ab1 could oxidize As(Ⅲ) quickly with the addition of organic carbon and oxygen. A co-culture system demonstrated mutualistic interactions where "T. sichuanensis" XZ-Cy5 secreted organic carbon to facilitate heterotrophic growth of Chelatococcus sp. XZ-Ab1, while Chelatococcus sp. XZ-Ab1 promoted growth of "T. sichuanensis" XZ-Cy5 by oxidizing toxic As(Ⅲ) to the less toxic arsenate. Following growth of the co-culture using [13]CO2, NanoSIMS isotope tracing provided direct evidence of photoautotroph-derived carbon from "T. sichuanensis" XZ-Cy5 to Chelatococcus sp. XZ-Ab1. Metagenomic and genomic analyses indicated several mechanisms for metabolic complementarity between the two strains, including As detoxification by the heterotroph and fixed carbon and nitrogen provision by the cyanobacterium, in addition to oxygen production. Our findings reveal a cooperative survival strategy in extreme environments and provide a novel model for engineering synthetic microbial consortia for As bioremediation.},
}

*Arsenic/metabolism/toxicity
*Microbial Consortia/physiology
Biodegradation, Environmental
Photosynthesis
*Cyanobacteria/metabolism
Hot Springs/microbiology
*Symbiosis
Inactivation, Metabolic
Oxidation-Reduction
Coculture Techniques

@article {pmid42780516,
year = {2026},
author = {Jiang, X and Shi, S and Li, M and Zhang, Y and Xing, G and Yan, Q and Li, S and Sun, W and Li, H},
title = {Fecal microbiota transplantation in adolescents with obesity induces limited and donor-dependent remodeling of the gut microbiome.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1927870},
pmid = {42780516},
issn = {1664-2392},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Adolescent ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; *Pediatric Obesity/therapy/microbiology ; Longitudinal Studies ; Metagenome ; },
abstract = {INTRODUCTION: Obesity is a global health challenge, and fecal microbiota transplantation (FMT) is considered a potential intervention; however, its long-term ecological impact remains unclear.

METHODS: In this 182-day longitudinal cohort of adolescents with obesity (378 samples), metagenomic sequencing was used to assess FMT-induced remodeling of the multi-kingdom gut ecosystem through species composition, diversity, microbial networks, and machine learning analyses.

RESULTS: FMT induced only transient shifts in community structure, with limited donor strain engraftment and strong resilience of recipient core taxa. Bacteria were the primary responders, the virome showed short-term perturbation, and network restoration was partial and donor-dependent.

DISCUSSION: FMT exerts limited, donor-dependent ecological effects in obese adolescents. Optimizing donor selection and personalized matching may be essential for improving long-term efficacy.},
}

Humans
*Fecal Microbiota Transplantation/methods
Adolescent
*Gastrointestinal Microbiome/physiology
Female
Male
*Pediatric Obesity/therapy/microbiology
Longitudinal Studies
Metagenome

@article {pmid42781813,
year = {2026},
author = {Astrin, JJ and Labuschagne, K and Avrili, H and Barker, K and Burger, AL and Dhyani, A and Escobari Vargas, B and Johnston, P and Pugh, RS and Grossman, GH and Conradie, EH},
title = {Where Worlds Align: Insights from the Joint GGBN-ISBER Conference on Biodiversity and Biobanking, Cape Town, October 2025.},
journal = {Biopreservation and biobanking},
volume = {},
number = {},
pages = {19475535261488949},
doi = {10.1177/19475535261488949},
pmid = {42781813},
issn = {1947-5543},
abstract = {The 2025 Joint GGBN-ISBER Conference in Cape Town united biodiversity, environmental, and biomedical biobanking communities from 38 countries. The event highlighted biobanks as interdisciplinary and collaborative infrastructures for addressing global challenges-pandemics, biodiversity loss, and food security, among others. Recurring themes throughout the conference were as follows: (1) Harmonization and Quality-adoption of best practices and standards where possible to ensure global interoperability and sample integrity; (2) Equitable Governance-crafting flexible, transparent frameworks for sample and data sharing that uphold sovereignty and benefit local communities; (3) Technological and Data Integration-using artificial intelligence, omics technologies, and standardized metadata to transform physical specimens into scalable digital resources; and (4) Resilient Infrastructure-securing long-term investment in regional biobanking networks and targeted training to build enduring capacity, embedding sustainability by design and safeguarding local knowledge.},
}

@article {pmid42189604,
year = {2026},
author = {Lopes, F and Martinez-Martinez, D and Späth, MR and Hoyer-Allo, KJR and Strubl, S and Cukoski, S and Knieps, L and Brodesser, S and Göbel, H and Schwarz, G and van den Berg, BM and Rabelink, TJ and Schermer, B and Benzing, T and Müller, RU and Beyer, A and Cabreiro, F and Koehler, FC},
title = {The Interplay between Gut Microbiota and Diet-Induced Kidney Protection.},
journal = {Kidney360},
volume = {7},
number = {9},
pages = {1930-1942},
pmid = {42189604},
issn = {2641-7650},
support = {RPG-2022-299//Leverhulme Trust/ ; 102532/Z/12/Z, 102531/Z/13/A/WT_/Wellcome Trust/United Kingdom ; EXC 2030 -390661388//Deutsche Forschungsgemeinschaft/ ; 2020_EKEA.121//Else Kröner-Fresenius-Stiftung/ ; 390661388//Deutsche Forschungsgemeinschaft/ ; RPG-2022-299//Leverhulme Trust/ ; 102532/Z/12/Z, 102531/Z/13/A/WT_/Wellcome Trust/United Kingdom ; EXC 2030 -390661388//Deutsche Forschungsgemeinschaft/ ; 2020_EKEA.121//Else Kröner-Fresenius-Stiftung/ ; 390661388//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Reperfusion Injury/microbiology/prevention & control ; *Gastrointestinal Microbiome/physiology ; Mice ; *Kidney/metabolism/pathology/blood supply ; Male ; *Caloric Restriction ; *Diet ; Mice, Inbred C57BL ; Disease Models, Animal ; *Acute Kidney Injury/prevention & control/microbiology ; },
abstract = {KEY POINTS: Beneficial diets changed the composition of gut microbiota in an ischemia-reperfusion injury‑dependent manner in rodents. Taxonomic and functional profiling revealed a central role of Lachnospiraceae , a main producer of microbially derived short-chain fatty acids. Comparative bulk transcriptomics suggested the metabolic use of these bacterial products as an additional energy source in kidneys of protected mice.

BACKGROUND: On one hand, dietary interventions are known for their pivotal role in regulating diversity, composition, and function of the gut microbiome. On the other hand, specific diets show an immense potential in preventing kidney injury from various damaging stimuli in rodents, and recent findings, in turn, highlight a central role of gut microbiota in kidney health and disease.

METHODS: Three protective dietary regimens-a fasting-mimicking diet, a diet depleted in sulfur-containing amino acids, and caloric restriction-were examined in parallel in a rodent model of ischemia-reperfusion injury (IRI). To delineate the diet-induced effect on gut microbiota in response to ischemic kidney damage, we used comparative shotgun metagenomics for taxonomic and functional profiling. We further examined the renal metabolic response using comparative transcriptomics to unravel the interplay between gut microbiota and kidney protection.

RESULTS: Beneficial dietary preconditioning strategies changed the composition of gut microbiota in an IRI-dependent manner. Using ternary plots to investigate the role of dietary interventions over time before and after ischemic insult, we detected a central role of Lachnospiraceae that commonly expanded in response to renal IRI in dietary preconditioned mice. Further functional profiling of gut microbiota in our model revealed an increase in plasma levels of bacterial-derived short-chain fatty acids in diet-induced kidney protection. Comparative bulk transcriptomics in our model, in turn, pointed toward the metabolic use of these bacterial-derived short-chain fatty acids in kidneys of protected mice.

CONCLUSIONS: Because proximal tubules lack sufficient glycolytic capacity, products of microbial metabolism may serve as an additional energy source to fulfill their high demands when withstanding ischemic damage. Our data shed light on a close interplay between gut microbiota and diet-induced kidney protection calling for further research at the crossroads of microbiology, metabolism, and molecular nephrology.},
}

Animals
*Reperfusion Injury/microbiology/prevention & control
*Gastrointestinal Microbiome/physiology
Mice
*Kidney/metabolism/pathology/blood supply
Male
*Caloric Restriction
*Diet
Mice, Inbred C57BL
Disease Models, Animal
*Acute Kidney Injury/prevention & control/microbiology

@article {pmid42298622,
year = {2026},
author = {Wang, F and Sang, Y and Guo, J and Fu, Y and Yang, M and Shan, F and Chen, Y and Zhang, S and Li, X and Li, J and Zhang, L},
title = {Dietary glycyrrhizic acid improves growth performance and modulates upper respiratory microbiota in weaned piglets.},
journal = {BMC veterinary research},
volume = {22},
number = {1},
pages = {},
pmid = {42298622},
issn = {1746-6148},
support = {231111111600//Henan Province Key Research and Development Plan Project/ ; 251111113300//Henan Province Key Research and Development Plan Project/ ; CARS-35//the National Pig Industry Technology System/ ; },
mesh = {Animals ; *Glycyrrhizic Acid/pharmacology/administration & dosage ; Swine/growth & development/microbiology ; Diet/veterinary ; Weaning ; Animal Feed/analysis ; *Microbiota/drug effects ; Dietary Supplements ; Female ; *Respiratory System/microbiology ; },
abstract = {BACKGROUND: Natural products with dual immunomodulatory and antimicrobial functions offer promising strategies to reduce antibiotic use in livestock. Glycyrrhizic acid (GA), the principal bioactive component of licorice, has demonstrated anti-inflammatory and antiviral properties, yet its translational potential in swine health remains underexplored. This study evaluated the efficacy of GA in weaned piglets under commercial nursery conditions as an antibiotic alternative. A total of 225 weaned piglets were assigned to five groups: negative control (CON, basal diet), farm routine (FA, conventional antibiotics), and three GA-supplemented groups (GLL, 0.65 g/kg; GLM, 1.3 g/kg; GLH, 2.6 g/kg).

RESULTS: The result showed that dietary GA supplementation (2.6 g/kg) numerically improved growth performance and reduced cough scores, although not statistically significant. GA significantly decreased the diarrhea index and improved skin scores. GA also significantly increased serum IgG and IgM levels in piglets and showed a trend toward higher IgA levels. Furthermore, GA exhibited a trend toward lowering serum IL‑1β levels while upregulating IFN‑γ and IL‑10 levels. Regarding antioxidant parameters, GA significantly upregulated T‑SOD, GSH‑PX, and CAT activities and downregulated LDH activity. Metagenomic analysis revealed that high‑dose glycyrrhizic acid (GA) significantly increased the abundance of Alloprevotella, while decreasing the abundances of Moraxella pluranimalium and 11 other pathogenic species associated with respiratory diseases and lung injury, including Glaesserella parasuis, Mesomycoplasma hyorhinis, Mesomycoplasma hyopneumoniae, Streptococcus suis, among others, thereby reshaping the upper respiratory tract microbiota of pigs.

CONCLUSIONS: Collectively, these findings support GA as a viable non-antibiotic strategy for improving immune function, antioxidant capacity, and respiratory health in weaned piglets.},
}

Animals
*Glycyrrhizic Acid/pharmacology/administration & dosage
Swine/growth & development/microbiology
Diet/veterinary
Weaning
Animal Feed/analysis
*Microbiota/drug effects
Dietary Supplements
Female
*Respiratory System/microbiology

@article {pmid42439467,
year = {2026},
author = {Luo, Y and Kang, FL and Li, QM and Yang, WC},
title = {Metagenomic Association Uncovers Host Genotype-Structured Rhizobacterial Networks and Novel Taxa That Enhance Soybean Salt Tolerance.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {53},
pages = {e76373},
pmid = {42439467},
issn = {2198-3844},
support = {YSBR-011//CAS project for Young Scientists in Basic Research/ ; 2023YFD1200600//National Key Research and Development Program of China/ ; XDA24010205//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDA26030105//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2016QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; },
mesh = {*Glycine max/genetics/microbiology/physiology ; *Salt Tolerance/genetics ; Rhizosphere ; Soil Microbiology ; *Metagenomics/methods ; Genotype ; *Microbiota/genetics ; Plant Roots/microbiology ; },
abstract = {Salinity is an escalating agricultural challenge, yet plant microbiomes offer a promising avenue for improving salt tolerance. Nevertheless, most naturally occurring microbes remain unevaluated for plant growth-promoting function, and systematic approaches to uncover salt-tolerance-enhancing plant growth-promoting rhizobacteria (PGPR) are limited. Here, using soybean as a model, we implement a quantitative framework to characterize rhizosphere microbial networks and nominate novel taxa functionally associated with plant salt tolerance. We introduced a salt tolerance index (STI) to quantify plant salt tolerance and normalize performance across heterogeneous natural soil salinity. Metagenomic sequencing and co-occurrence analysis revealed distinct rhizosphere microbiota structures between tolerant and susceptible soybeans. In tolerant soybeans, Pseudomonas dominated as the hub of a highly interconnected network, whereas susceptible accessions showed a fragmented network dominated by Acinetobacter. Correlation analyses identified bacterial taxa positively associated with STI, including documented salt-tolerant PGPR and novel candidates. Greenhouse experiments showed that one candidate, Thalassospira xiamenensis, enhances soybean salt tolerance and reshapes host ion-transport and oxidative-stress gene expression under salinity, validating our screening strategy. Our culture-independent metagenomic association approach reveals host genotype-structured rhizosphere microbial networks underlying salt tolerance and provides an efficient, labor-saving means for high-throughput identification of salt-tolerant PGPR.},
}

*Glycine max/genetics/microbiology/physiology
*Salt Tolerance/genetics
Rhizosphere
Soil Microbiology
*Metagenomics/methods
Genotype
*Microbiota/genetics
Plant Roots/microbiology

@article {pmid42485926,
year = {2026},
author = {de Bruijn, DGJ and Gusinac, A and Ederveen, THA and Le, ND and Kulkarni, P and Meijer, RI and Janssen, MCH and Zweers, HEE},
title = {Gut microbiota alterations in individuals with mitochondrial disease caused by the m.3243A >G mutation.},
journal = {Molecular genetics and metabolism},
volume = {149},
number = {1-2},
pages = {110208},
doi = {10.1016/j.ymgme.2026.110208},
pmid = {42485926},
issn = {1096-7206},
mesh = {Humans ; *Mitochondrial Diseases/genetics/microbiology ; Female ; Male ; Diabetes Mellitus, Type 1/microbiology/genetics ; Adult ; *Gastrointestinal Microbiome/genetics ; Mutation ; *DNA, Mitochondrial/genetics ; Deafness/genetics/microbiology ; Ruminococcus/isolation & purification/genetics ; Faecalibacterium prausnitzii/isolation & purification/genetics ; Escherichia coli/isolation & purification/genetics ; Feces/microbiology ; Case-Control Studies ; *Dysbiosis/microbiology/genetics ; Middle Aged ; Adolescent ; Young Adult ; Eubacteriales ; },
abstract = {People with mitochondrial disease (MD) associated with the m.3243 A > G mutation often experience gastrointestinal complaints and dysmotility, suggesting dysbiosis of the gut microbiome. A common phenotype of the m.3243 A > G mutation is Maternally Inherited Diabetes and Deafness (MIDD). Previous studies have shown that other forms of diabetes are associated with an altered gut microbiome. Therefore, our study aimed to investigate the gut microbiota of people with MD caused by the m.3243 A > G mutation compared to healthy controls (Lifelines®) and people with type 1 diabetes (T1D). Fecal samples of 30 people with the m.3243 A > G mutation were used for shotgun metagenomic sequencing. The MD group was compared with 60 healthy controls and 60 people with T1D from different datasets, and were matched for age, sex, and BMI. We found that the Bray-Curtis β-diversity of the gut microbiota differed significantly between MD compared to healthy controls and T1D, while there was a non-significant reduction in Shannon α-diversity in the MD group. The gut microbiota of the MD group was characterized by reduced Faecalibacterium prausnitzii, and increased Escherichia coli, Ruminococcus gnavus, and Ruminococcus torques levels compared to healthy controls and T1D. This pattern aligns with microbial signatures reported in inflammatory bowel disease, which is associated with mitochondrial dysfunction in intestinal epithelial cells. Overall, our explorative study suggest that people with the m.3243 A > G mutation exhibit a dysbiotic gut microbiota, which may pave the way for future research aimed at developing new therapies, dietary adjustments and their potentials to improve quality of life.},
}

Humans
*Mitochondrial Diseases/genetics/microbiology
Female
Male
Diabetes Mellitus, Type 1/microbiology/genetics
Adult
*Gastrointestinal Microbiome/genetics
Mutation
*DNA, Mitochondrial/genetics
Deafness/genetics/microbiology
Ruminococcus/isolation & purification/genetics
Faecalibacterium prausnitzii/isolation & purification/genetics
Escherichia coli/isolation & purification/genetics
Feces/microbiology
Case-Control Studies
*Dysbiosis/microbiology/genetics
Middle Aged
Adolescent
Young Adult
Eubacteriales

@article {pmid42677482,
year = {2026},
author = {Wu, Q and Xu, X and Guo, Y and Li, H and Hao, Y and Zhang, Z and Cai, Z and White, JC and Ma, C},
title = {Nano-boron nitride enhances soybean growth and symbiotic nitrogen fixation by modulating the rhizosphere microbiome and biogeochemical cycling.},
journal = {Nanoscale},
volume = {18},
number = {36},
pages = {19815-19829},
doi = {10.1039/d6nr02400a},
pmid = {42677482},
issn = {2040-3372},
mesh = {*Glycine max/growth & development/microbiology/drug effects/metabolism ; *Nitrogen Fixation/drug effects ; *Rhizosphere ; *Microbiota/drug effects ; *Boron Compounds/chemistry/pharmacology ; Symbiosis/drug effects ; Biomass ; },
abstract = {Nanotechnology offers promising strategies for sustainable agriculture, yet the systemic mechanisms by which nanomaterials enhance legume nitrogen fixation remain insufficiently understood. The multi-scale impacts of nano-boron nitride (nano-BN) on soybean growth, biological nitrogen fixation, and rhizosphere microbial communities were investigated. Soil addition of 50 mg kg[-1] nano-BN significantly promoted plant biomass, nodule biomass, and leghemoglobin content by 10.0%, 27.4%, and 39.4%, respectively, compared to the untreated control. Nano-BN also enhanced the NH4[+]-N and NO3[-]-N content by 24.3% and 19.9% in root tissues, while reducing these levels in rhizosphere soil. Additionally, nano-BN enriched rhizosphere-dissolved organic matter, particularly humic-like components. Metagenomic analysis revealed that nano-BN reshaped carbon and nitrogen cycling functional genes, enhancing CO2 fixation and aerobic respiration; the nitrogen fixation functional gene nifH was upregulated by 27.7%. Microbial community analysis demonstrated increased bacterial diversity and abundance of beneficial taxa, particularly Bradyrhizobium, which increased by 24.9%. Co-occurrence network analysis revealed enhanced positive interactions and greater topological complexity upon the addition of nano-BN compared to the untreated control, indicating improved community stability. Collectively, these findings demonstrate that nano-BN promotes soybean growth through integrated regulation of nutrient cycling, symbiotic nitrogen fixation, and rhizosphere microbiome assembly. Nano-BN represents an innovative nano-fertilization strategy for enhancing biological nitrogen fixation, improving nutrient use efficiency, and advancing sustainable agricultural systems.},
}

*Glycine max/growth & development/microbiology/drug effects/metabolism
*Nitrogen Fixation/drug effects
*Rhizosphere
*Microbiota/drug effects
*Boron Compounds/chemistry/pharmacology
Symbiosis/drug effects
Biomass

@article {pmid42684889,
year = {2026},
author = {Mueller, NT and Xiao, S and Liu, T and Debelius, J and Kress, AM and Zhao, N and Moore, B and McKee, KS and Jacobson, LP and Comstock, SS and , },
title = {Mother-infant sharing of gut and vaginal microbes at the species and strain level.},
journal = {Cell reports},
volume = {45},
number = {9},
pages = {117920},
doi = {10.1016/j.celrep.2026.117920},
pmid = {42684889},
issn = {2211-1247},
mesh = {Female ; Humans ; *Vagina/microbiology ; Infant ; *Gastrointestinal Microbiome/genetics ; Mothers ; Pregnancy ; Microbiota ; Infant, Newborn ; },
abstract = {Mother-to-offspring microbial transmission is a foundational process for seeding the infant gut microbiome, yet the relative contributions of maternal body sites and the influence of birth delivery mode remain incompletely understood. We use shotgun metagenomic sequencing in 68 mother-infant dyads to investigate species- and strain-level sharing of the maternal gut and vaginal microbiomes with the infant gut during the first year of life. At 2-4 months of age, infants share an average of 35% of species with their mother's microbiomes, with markedly greater sharing from the maternal gut than the vagina. Vaginally delivered infants exhibit higher levels of sharing than those born by cesarean section (C-section). Strain-level analyses reveal persistent mother-infant transmission across multiple Bacteroides and Bifidobacterium species genome bins, with strain-sharing frequencies varying by species and birth mode. C-section reduces the extent of mother-infant species- and strain-level sharing.},
}

Female
Humans
*Vagina/microbiology
Infant
*Gastrointestinal Microbiome/genetics
Mothers
Pregnancy
Microbiota
Infant, Newborn

@article {pmid42709542,
year = {2026},
author = {Pinedo-Bardales, M and Erreygers, I and Allonsius, CN and Hiel, M and Eilers, T and Van Rillaer, T and Gehrmann, T and Ahannach, S and Dillen, J and De Boeck, I and Verhoeven, V and Van Puyvelde, S and Segata, N and Wittouck, S and Lebeer, S},
title = {Species and strain sharing in the vaginal microbiome of mothers and their adult daughters.},
journal = {Cell reports},
volume = {45},
number = {9},
pages = {117942},
pmid = {42709542},
issn = {2211-1247},
mesh = {Female ; *Microbiota/genetics ; *Vagina/microbiology ; Humans ; *Mothers ; Adult ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Nuclear Family ; *Lactobacillus crispatus/genetics/isolation & purification ; Species Specificity ; },
abstract = {The vaginal microbiome is key for women's health. However, its establishment, interindividual variation and dynamics remain poorly understood. Here, we investigate bacterial relatedness at species and strain level in adult mother-daughter pairs from the large-scale citizen-science program Isala. Using metagenomic sequencing with quality control including 16S rRNA profile comparison, along with targeted culturing, we assess intergenerational microbiome sharing. At species level, daughters' vaginal microbiomes are significantly more similar to their mothers' than to those of unrelated mothers, with a strong mother-daughter correlation in Lactobacillus crispatus dominance. Strain-level analyses of metagenomes and isolate genomes reveal intraspecies diversity in L. crispatus, with up to two strains observed within the same host, and support intergenerational vaginal bacteria sharing. SNV counts in shared L. crispatus strains show no correlation with daughters' ages. Together, these findings suggest that maternal transmission, host factors, and (shared) environment collectively shape the vaginal microbiome, providing fundamental ecological insights into vaginal microbiome dynamics and perspectives toward lactobacilli-based applications.},
}

Female
*Microbiota/genetics
*Vagina/microbiology
Humans
*Mothers
Adult
RNA, Ribosomal, 16S/genetics
Metagenome
Nuclear Family
*Lactobacillus crispatus/genetics/isolation & purification
Species Specificity

@article {pmid42772437,
year = {2026},
author = {Kang, D and Ji, Y and Cao, Y and Ou, J and Yang, Q},
title = {Grazing and soil moisture transitions reorganize cross-library co-abundance modules of resistance and virulence genes in alpine wetland soils.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129221},
doi = {10.1016/j.envpol.2026.129221},
pmid = {42772437},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs), heavy-metal resistance genes (HMRGs) and virulence factor genes (VFGs) can coexist in soils, yet their joint responses to hydrological and grazing pressures remain unclear. We combined shotgun metagenomics, a unified co-abundance network, fixed-module environmental-stratum deletion, threshold modelling, and contig, metagenome-assembled genome (MAG) and mobile genetic element (MGE) annotations across 32 alpine wetland plots spanning continuous soil water content and two grazing intensities. The unified network identified 14 representative cross-library hubs and four candidate modules whose coordinated states explained peripheral coactivation better than individual hubs, with M01-M03 showing more consistent support across sensitivity analyses than M04. All modules retained all three gene libraries after grazing- or moisture-stratum deletion, but connectivity, occupancy and cross-edge activity changed in module-specific ways. Within this dataset, a candidate soil-water-content transition near 89.4% separated contrasting responses and revealed partial decoupling between sample-level activation and cross-sample topology. Carrier support was heterogeneous, with M03 showing the strongest partial MAG- and MGE-associated support, whereas mobility-related responses varied among modules and environments. Overall, grazing and moisture reorganized rather than uniformly intensified these gene assemblages. Co-abundance and carrier association indicate genomic organization and mobility-related potential, not realized pollution risk or horizontal transfer.},
}

@article {pmid42776951,
year = {2026},
author = {Hu, A and Liu, J and Chen, P and Yang, K and Xu, F and Luo, G and Zhang, J and He, M},
title = {Gut microbiome is associated with stereotypic behavior of the giant panda (Ailuropoda melanoleuca).},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357625},
pmid = {42776951},
issn = {1932-6203},
mesh = {Animals ; *Ursidae/microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; *Stereotyped Behavior/physiology ; Feces/microbiology ; *Behavior, Animal ; Male ; },
abstract = {The giant panda (Ailuropoda melanoleuca) is a relict species endemic to China. Captive breeding has boosted its population. However, some captive individuals exhibit stereotypic behavior. Though extensive research showing that host behavior can be influenced by gut microbiota via the gut-brain axis, the gut microbiota related to stereotypic behavior of giant pandas has not been reported. To explore gut microbial composition and functional characteristics of stereotypically behaving (SB) giant pandas, the behavior of 15 captive giant pandas was observed, and their feces were analyzed using 16S ribosomal RNA (rRNA) sequencing (n = 145) and metagenomic sequencing (n = 45). Our study revealed distinct gut microbial diversity, composition, and functions between SB giant pandas and normal controls, indicating gut microbial dysbiosis in SB giant pandas. Serratia sp. Se-RSBMAAmG was significantly enriched in SB giant pandas, five Clostridium species and Lactococcus garvieae exhibited upward trends in SB individuals, whereas the probiotic Enterococcus hirae showed the opposite trend compared with those in normal controls. The Clostridium bacteria may affect propionate metabolism and the gamma-aminobutyric acidergic (GABAergic) synapse pathway, potentially affecting the emergence of stereotypic behavior. These findings suggest a link between gut microbiota and stereotypic behavior of giant pandas, providing novel insights for their conservation.},
}

Animals
*Ursidae/microbiology/physiology
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
*Stereotyped Behavior/physiology
Feces/microbiology
*Behavior, Animal
Male

@article {pmid42778553,
year = {2026},
author = {Meng, JX and Li, WD and Tao, WF and Tu, S and Gao, J and Zhao, X and Li, J and Wu, J and Liu, C and Zhang, Y and Zhu, SJ},
title = {An atlas of colonization factors in the human gut microbiome reveals ecological strategies and inflammatory bowel disease signatures.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42778553},
issn = {2041-1723},
support = {82572567//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology ; *Gastrointestinal Microbiome/genetics/physiology ; Metagenome ; Metagenomics ; Dysbiosis/microbiology ; Phylogeny ; *Bacteria/genetics/classification/isolation & purification ; },
abstract = {Long-term residence in the gut enables microbes to interact with the host and influence intestinal health. However, many microbiome studies focus on taxonomic profiles or broad metabolic pathway annotations and provide limited insight into the conserved genes that support microbial residence. Here we show that colonization factors (CFs), defined as gut-enriched genes associated with microbial residence, offer a colonization-centered functional framework for profiling the human gut microbiome. By mapping 79 CF families across 289,231 surveyed microbial genomes, we identify more than seven million CF homologs and reveal their widespread distribution, phylogenetically structured organization and functional stratification into three putative lineage-associated colonization strategies centered on metabolism, stress resistance and microbial communication. Applying this framework to 3,666 metagenomic and metatranscriptomic samples from 10 inflammatory bowel disease (IBD) cohorts, we find that disease-associated dysbiosis is accompanied by recurrent remodeling of CF repertoires. These alterations can be traced to specific colonization-associated functions and microbial carrier species, and are captured by a compact feature panel that discriminates disease status within cohorts. These results establish CF profiling as a mechanism-oriented approach for interpreting the ecological organization of the gut microbiome and prioritizing colonization-associated targets for future disease monitoring and intervention studies.},
}

Humans
*Inflammatory Bowel Diseases/microbiology
*Gastrointestinal Microbiome/genetics/physiology
Metagenome
Metagenomics
Dysbiosis/microbiology
Phylogeny
*Bacteria/genetics/classification/isolation & purification

@article {pmid42778565,
year = {2026},
author = {Lv, Y and Liu, P and Liu, Y and Dong, L and Li, J and Zhang, Y},
title = {Redox-stratified macromolecule degradation supports microbial survival in the oligotrophic Kermadec Trench sediments.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42778565},
issn = {2041-1723},
support = {42188102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42122043//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Geologic Sediments/microbiology ; Oxidation-Reduction ; Metagenome ; *Bacteria/genetics/metabolism/classification ; Ecosystem ; Phylogeny ; *Microbiota/genetics ; Pacific Ocean ; },
abstract = {Kermadec Trench is a hadal ecosystem in the South Pacific with the water depth 10,047 m. The trench bottom harbors a highly active and populated microbial community, despite the surface sediment is characterized as extremely pressurized, oligotrophic and with low oxygen concentration. It is intriguing, as well as technically challenging, to investigate the microbial adaptation strategies therein. Here we performed the in situ RNA fixation on sediment samples with the assistant of Fendouzhe manned submersible, to approach natural status of microbial metabolisms on both genomic and transcriptomic levels. We reconstructed 1369 metagenome-assembled genomes (MAGs), revealing dominant heterotrophic lineages encoding carbohydrate-active enzymes targeting complex macromolecules such as peptidoglycan and β-1,4-mannan. These degradation processes were transcriptionally coupled with flexible respiratory pathways utilizing oxygen, nitrate, and nitrite as electron acceptors. Co-expression analyses and microbial co-occurrence networks demonstrated niche partitioning driven by redox stratification, with slope communities favoring oxidative pathways and bottom communities enriched in reductive metabolisms, including denitrification and N2O reduction. Despite compositional divergence, both habitats exhibited conserved functional strategies centered on macromolecule recycling and redox-coupled respiration. Our findings highlight a coordinated system of organic matter remineralization and electron acceptor versatility that underpins microbial survival in Earth's deepest seafloor ecosystems.},
}

*Geologic Sediments/microbiology
Oxidation-Reduction
Metagenome
*Bacteria/genetics/metabolism/classification
Ecosystem
Phylogeny
*Microbiota/genetics
Pacific Ocean

@article {pmid42780152,
year = {2026},
author = {Cui, D and Ren, X and Li, N},
title = {Integrating metagenomics, transcriptomics, and molecular docking to reveal core gene biomarkers and gut microbiota regulatory mechanisms in tuberculous meningitis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1844914},
pmid = {42780152},
issn = {1664-3224},
mesh = {Humans ; *Tuberculosis, Meningeal/microbiology/genetics/metabolism/immunology ; Molecular Docking Simulation ; *Metagenomics/methods ; *Gastrointestinal Microbiome/immunology ; Biomarkers ; Female ; Male ; Gene Expression Profiling ; *Transcriptome ; Dysbiosis/microbiology ; Adult ; Macrophages/immunology/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {PURPOSE: Tuberculous meningitis (TBM) is a severe extrapulmonary tuberculosis with high mortality and neurological sequelae, while the role of gut microbiota and its metabolites in TBM pathogenesis remains poorly understood. This study aimed to characterize gut microbiota alterations in TBM patients and elucidate the "microbiota-metabolite-gene" regulatory axis.

METHODS: Fecal samples from 11 TBM patients and 11 healthy controls were subjected to 16S rRNA sequencing. Core target genes were identified via differential expression screening, machine learning, immune infiltration analysis and gene set enrichment analysis based on the public GSE40586 dataset. The regulatory axis was constructed by database prediction and molecular docking, and the regulatory effect was verified by in vitro functional assays in THP-1-derived macrophages.

RESULTS: TBM patients exhibited significant gut dysbiosis. Two core genes (PIK3CB and JAK2) were identified, which were positively correlated with pro-inflammatory immune cells and enriched in bacterial infection pathways. The constructed regulatory axis showed that upregulated gut bacteria produced bile acid metabolites targeting PIK3CB/JAK2, with strong binding affinity verified by molecular docking. In vitro experiments verified that CDCA dose-dependently upregulated PIK3CB and JAK2 expression and promoted pro-inflammatory activation of macrophages, while silencing of target genes significantly reversed this effect.

CONCLUSION: This study identifies a "gut microbiota-bile acid-PIK3CB/JAK2" regulatory axis in TBM, thus providing novel insights into gut-brain crosstalk and potential diagnostic biomarkers and therapeutic targets.},
}

Humans
*Tuberculosis, Meningeal/microbiology/genetics/metabolism/immunology
Molecular Docking Simulation
*Metagenomics/methods
*Gastrointestinal Microbiome/immunology
Biomarkers
Female
Male
Gene Expression Profiling
*Transcriptome
Dysbiosis/microbiology
Adult
Macrophages/immunology/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid42780395,
year = {2026},
author = {Ma, C and Lei, S and Zhang, G and Hu, X and Qiu, X and Wang, Q and Kang, X},
title = {Multiorgan and gut microbial alterations in ovariectomized mice: a multiomics analysis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1847257},
doi = {10.3389/fimmu.2026.1847257},
pmid = {42780395},
issn = {1664-3224},
mesh = {Animals ; *Ovariectomy ; Female ; Multiomics ; *Gastrointestinal Microbiome ; Mice ; Liver/metabolism ; Metabolomics/methods ; Colon/metabolism/microbiology ; Muscle, Skeletal/metabolism ; Metabolome ; Mice, Inbred C57BL ; Transcriptome ; },
abstract = {INTRODUCTION: Postmenopausal metabolic dysfunction is increasingly recognized as a multisystem disorder associated with estrogen deficiency, yet how gut microbial, metabolic, and tissue-level alterations co-occur across organs remains incompletely characterized.

METHODS: Here, we used an ovariectomy (OVX) mouse model and an integrated multiomics strategy to characterize systemic alterations in gut microbiota, metabolites in colonic contents and circulation, and tissue-level molecular profiles across the colon, liver, skeletal muscle, and bone.

RESULTS: OVX mice showed higher body weights at multiple postoperative time points, lower serum estradiol concentrations, differences in selected inflammatory and bone-turnover markers, representative histological differences across multiple tissues, and OVX-Sham differences in femoral microarchitecture. Shotgun metagenomic profiling showed significant differences in gut microbial composition, with lower evenness-sensitive diversity and differences in dominant taxa. Metabolomic profiling of colonic contents demonstrated global differences in the luminal metabolic profile, including lower relative abundances of major short-chain fatty acids, differences in bile acid composition, and prominent tryptophan-related features. At the host interface, colonic transcriptomic analysis identified annotations related to epithelial membrane polarity, vesicle trafficking, endoplasmic reticulum protein processing, and bile acid- and energy-sensing pathways. Among the 19 differential circulating bile acids and short-chain fatty acids, most were lower in OVX mice. Feature-level analyses identified multiple hepatic metabolite and bile acid differences, whereas the hepatic transcriptome did not show significant global separation; differential-expression and gene-set enrichment analyses nonetheless identified selected differences related to lipid metabolism, energy metabolism, and molecular transport. Distal tissues also displayed molecular differences, including a significant global transcriptomic difference in skeletal muscle and a significant global metabolomic difference in bone; differential bone metabolites were annotated to energy-, amino-acid-, lipid-, and cyclic guanosine monophosphate-protein kinase G (cGMP-PKG)-related pathways.

DISCUSSION: Collectively, these findings define a gut-associated, multiorgan pattern of OVX-related remodeling characterized by concurrent microbial, metabolite, and tissue-level differences. This descriptive, associative, and hypothesis-generating dataset provides a reference for future studies testing the relevance of these OVX-associated patterns to menopause-associated metabolic dysfunction.},
}

Animals
*Ovariectomy
Female
Multiomics
*Gastrointestinal Microbiome
Mice
Liver/metabolism
Metabolomics/methods
Colon/metabolism/microbiology
Muscle, Skeletal/metabolism
Metabolome
Mice, Inbred C57BL
Transcriptome

@article {pmid42271018,
year = {2026},
author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG},
title = {Disruption of the spinal cord-gut axis alters microbial dynamics and carbohydrate cross-feeding in the gut.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42271018},
issn = {2399-3642},
support = {890085//Craig H. Neilsen Foundation (Neilsen Foundation)/ ; ABI#2149505//National Science Foundation (NSF)/ ; DBI#2022070//National Science Foundation (NSF)/ ; },
mesh = {Animals ; Female ; Mice, Inbred C57BL ; Mice ; Male ; *Gastrointestinal Microbiome ; *Spinal Cord/physiology ; *Spinal Cord Injuries/microbiology/metabolism ; Metagenome ; *Carbohydrate Metabolism ; Metagenomics ; },
abstract = {Spinal cord-gut communication regulates gut bacteria, yet the underlying mechanisms remain poorly understood. Previous studies relied primarily on gene markers with limited functional analysis or genome-resolved snapshots from small cohorts. Here, we assessed microbiome dynamics via genome-resolved metagenomics on 333 samples from male and female C57BL/6 mice collected before and up to six months after surgical disruption of the spinal cord-gut axis. This resulted in 6,635 microbial draft genomes as a foundation for a new "Mouse B6 Gut Catalog" that significantly expands species and strain representation for this widely used laboratory mouse strain. Sampling revealed that disrupted spinal cord-gut signaling causes persistent, lesion-severity-, sex-, and time-specific shifts in microbial community composition, with consistent depletion of Lactobacillus johnsonii. Feeding purified L. johnsonii to spinal cord-injured mice prevented metabolic defects and systemic inflammation caused by disruption of the spinal cord-gut axis. Analyses using genome-resolved and community-based metabolic profiling indicated altered carbohydrate sharing and utilization of gut microbes, potentially depleting L. johnsonii, providing a genome-inferred mechanism for future hypothesis testing. This study improves murine microbiome catalogs, illustrates how metagenome-informed microbial interventions can provide a mechanistic understanding to improve host health, and underscores the vital role of a healthy spinal cord in regulating gut ecosystem function.},
}

Animals
Female
Mice, Inbred C57BL
Mice
Male
*Gastrointestinal Microbiome
*Spinal Cord/physiology
*Spinal Cord Injuries/microbiology/metabolism
Metagenome
*Carbohydrate Metabolism
Metagenomics

@article {pmid42560056,
year = {2026},
author = {Bernate, E and Shi, Y and Franck, E and Crofts, TS},
title = {A functionally selected Acinetobacter sp. phosphoethanolamine transferase gene from the goose fecal microbiome confers colistin resistance in E. coli.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {9},
pages = {e0246825},
pmid = {42560056},
issn = {1098-5336},
support = {7004080//National Institute of Food and Agriculture/ ; },
mesh = {*Colistin/pharmacology ; Animals ; *Escherichia coli/drug effects/genetics ; *Acinetobacter/genetics/enzymology ; *Anti-Bacterial Agents/pharmacology ; *Feces/microbiology ; *Drug Resistance, Bacterial/genetics ; *Ethanolaminephosphotransferase/genetics/metabolism ; *Microbiota ; *Bacterial Proteins/genetics/metabolism ; },
abstract = {Polymyxins are last-resort antibiotics for infections caused by multidrug-resistant gram-negative bacteria such as Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii. This makes the rise of bacteria exhibiting polymyxin E (colistin) resistance, largely through modification of lipid A moieties, concerning and suggests that it is important to document the potential sources of the corresponding resistance genes. This study searched for potential emerging colistin resistance genes from the environment by investigating a previously performed functional metagenomic selection for colistin resistance of a goose fecal microbiome. We found that the selection captured Acinetobacter sp. DNA fragments that all contained eptA genes. We confirmed their ability to confer significant colistin resistance in Escherichia coli via modification of lipid A in the outer membrane. Furthermore, we found evidence for mobilization of closely related eptA genes in Acinetobacter genomes, marking them as potential mcr genes or their precursors. This study highlights the potential for functional metagenomic selections for colistin resistance to capture genes from unexpected environmental sources such as the goose fecal microbiome.IMPORTANCEColistin is an important antibiotic of last resort, and increasing resistance to this drug via mobile phosphoethanolamine transferase genes, such as mcr-1, threatens its clinical utility. Given the discovery of mcr-1 in pigs, the ability of animals to act as vectors in the spread of colistin resistance is alarming. We show here that functionally selected Acinetobacter phosphoethanolamine transferase genes from the goose microbiome have the ability to confer clinical levels of colistin resistance when transferred into E. coli. While the genes are annotated as eptA homologs, closer study of these genes suggests that they may be mobilized within the Acinetobacter genus, suggesting that they may be mcr genes of concern instead.},
}

*Colistin/pharmacology
Animals
*Escherichia coli/drug effects/genetics
*Acinetobacter/genetics/enzymology
*Anti-Bacterial Agents/pharmacology
*Feces/microbiology
*Drug Resistance, Bacterial/genetics
*Ethanolaminephosphotransferase/genetics/metabolism
*Microbiota
*Bacterial Proteins/genetics/metabolism

@article {pmid42772323,
year = {2026},
author = {Li, SS and Niu, YH and Yu, HJ},
title = {A retrospective metagenomic analysis of fecal microbiota transplantation donors from five countries: Safety considerations for donor screening and core microbiome profiles of qualified donors.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {9},
pages = {e2604010},
doi = {10.71150/jm.2604010},
pmid = {42772323},
issn = {1976-3794},
support = {//Shanghai Engineering Research Center of Innovative Probiotic Drugs/ ; },
mesh = {Humans ; Retrospective Studies ; *Fecal Microbiota Transplantation/adverse effects ; *Metagenomics ; *Feces/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Canada ; New Zealand ; Netherlands ; China ; United States ; *Tissue Donors ; *Donor Selection ; Virulence Factors/genetics ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; },
abstract = {Fecal microbiota transplantation (FMT) has been successfully applied on clinical aspects, but its clinical outcomes remain unpredictable due to inconsistent donor screening protocols across hospitals, institutions, and countries. Hence, a retrospective analysis of metagenomic data from published studies on FMT donors via a unified bioinformatics workflow might contribute to the understanding of the safety considerations for donor screening and the fecal microbial profiles of qualified donors. In this study, we reanalyzed metagenomic data of 475 screened donor fecal samples from 24 studies spanning China, the USA, Canada, New Zealand, and the Netherlands. The genomic safety risks were evaluated by profiling antibiotic resistance genes (ARGs) and virulence factors (VFs), the results of which showed that no major toxin-associated virulence genes, such as Shiga toxin, Shiga-like toxin, or botulinum neurotoxin (BoNTs) genes harbored in the detected Escherichia coli, Clostridium butyricum, and Streptococcus pneumoniae, but several high-risk ARGs remained insufficiently addressed. The distribution of ARG-harboring bacteria in eligible FMT donors was country-specific. The alpha-diversity and microbial community structure were comparable between donor fecal samples from China and the USA. Interestingly, the core microbiome in fecal samples from Canada, the Netherlands, and New Zealand formed a single guild, while that from China and the USA formed two guilds, with predominantly positive intra-guild and negative inter-guild correlations, indicating that the co-abundance patterns of the core microbiome were conserved among certain countries. Furthermore, an exploratory retrospective classifier was developed based on core microbiome profiles to distinguish eligible FMT donors from general healthy individuals. These results provide evidence for integrating metagenomic sequencing into future FMT donor screening strategies.},
}

Humans
Retrospective Studies
*Fecal Microbiota Transplantation/adverse effects
*Metagenomics
*Feces/microbiology
*Bacteria/genetics/classification/isolation & purification
Canada
New Zealand
Netherlands
China
United States
*Tissue Donors
*Donor Selection
Virulence Factors/genetics
*Metagenome
*Gastrointestinal Microbiome/genetics
*Microbiota/genetics

@article {pmid42566872,
year = {2026},
author = {Pei, Y and Xu, Z and Xie, L and Wang, H},
title = {Enrichment of bile salt hydrolase-producing bacteria mediated by tetracycline resistance genes is associated with intestinal barrier damage in Rana chensinensis tadpoles.},
journal = {Ecotoxicology and environmental safety},
volume = {323},
number = {},
pages = {120624},
doi = {10.1016/j.ecoenv.2026.120624},
pmid = {42566872},
issn = {1090-2414},
mesh = {Animals ; Larva/drug effects/microbiology ; Intestinal Barrier Function/drug effects ; *Amidohydrolases/metabolism/genetics ; Bile Acids and Salts/metabolism ; *Tetracycline Resistance/genetics ; *Ranidae/microbiology ; *Intestines/drug effects/pathology ; *Tetracycline/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/genetics/drug effects/enzymology ; *Water Pollutants, Chemical/toxicity ; *Anti-Bacterial Agents/toxicity ; },
abstract = {Tetracycline (TET) is a pervasive contaminant in aquatic environments, yet how it reshapes gut microbiota composition and function to influence bile acid (BA) profiles and intestinal health remains poorly understood. In this study, Rana chensinensis tadpoles at Gosner stage 26 (Gs26) were exposed to environmentally relevant concentrations of tetracycline hydrochloride (10 and 100 μg/L) until metamorphic climax Gs38 and examined using a multi-pronged approach integrating histological analysis, intestinal targeted BA metabolomics, and fecal metagenomic sequencing. Our results showed that TET exposure disrupted intestinal barrier integrity in a dose-dependent manner, as evidenced by reduced enterocyte height, widened intercellular spaces, and irregular nuclear morphology. Metagenomic profiling revealed that TET treatment significantly enriched tetracycline resistance genes (e.g., tet(Q), tet(T), tetA(46), tetA(60)), which was accompanied by an increased abundance of bile salt hydrolase (BSH)-producing bacteria, including Bacteroides, Parabacteroides, and Vibrio. This microbial shift was accompanied by enhanced BA deconjugation, as reflected by a significantly increased ratio of unconjugated to conjugated BAs (p < 0.01). Notably, the enhanced deconjugation activity was paralleled by a marked accumulation of the hydrophobic and cytotoxic BA, chenodeoxycholic acid (CDCA) (p < 0.001), which was accompanied by a 73.9% reduction in total BA levels - a pattern that may reflect Farnesoid X Receptor (FXR)-mediated negative feedback regulation of hepatic BA synthesis, although this pathway was not directly examined. Furthermore, elevated CDCA levels were associated with intestinal histopathological damage. Collectively, these findings suggest a potential mechanistic cascade in which TET-induced enrichment of antibiotic resistance genes is associated with the expansion of BSH-active microbiota, together with disrupted BA homeostasis and compromised intestinal barrier function in amphibians. Causal relationships within this cascade await functional validation. Our study highlights the hidden ecological risks of antibiotic contamination in aquatic ecosystems and underscores the need for further molecular investigations into the signaling pathways involved.},
}

Animals
Larva/drug effects/microbiology
Intestinal Barrier Function/drug effects
*Amidohydrolases/metabolism/genetics
Bile Acids and Salts/metabolism
*Tetracycline Resistance/genetics
*Ranidae/microbiology
*Intestines/drug effects/pathology
*Tetracycline/toxicity
*Gastrointestinal Microbiome/drug effects
*Bacteria/genetics/drug effects/enzymology
*Water Pollutants, Chemical/toxicity
*Anti-Bacterial Agents/toxicity

@article {pmid42615618,
year = {2026},
author = {Hutchinson, NT and Maino-Vieytes, CA and Valls, C and Allen, J and Rund, LA and Johnson, RW and Woods, JA},
title = {Fermentation capacity of the gut microbiota influences exercise motivation and neuroendocrine integration.},
journal = {mSystems},
volume = {11},
number = {9},
pages = {e0087626},
pmid = {42615618},
issn = {2379-5077},
mesh = {Animals ; *Motivation/physiology ; Mice ; Mice, Inbred C57BL ; *Fermentation ; *Gastrointestinal Microbiome/physiology/drug effects ; Male ; *Physical Conditioning, Animal/physiology ; *Neurosecretory Systems/physiology/metabolism ; Prebiotics ; Corticosterone/blood ; Fatty Acids, Volatile/metabolism ; },
abstract = {UNLABELLED: Physical inactivity contributes substantially to global disease burden, yet the physiological mechanisms underlying exercise motivation remain poorly understood. The gut-brain axis presents a potentially modifiable target for behavioral intervention. Emerging evidence demonstrates that the gut microbiota influences motivated behaviors, but the specific metabolic functions and physiological mechanisms mediating these effects remain poorly defined. Here, we demonstrate that the predicted fermentation capacity of the gut microbiota influences voluntary wheel running (VWR) acquisition and neuroendocrine integration during exercise in C57BL/6J mice. Antibiotic-induced microbiome depletion reduced VWR acquisition, while shifting predicted function toward aerobic respiration and away from anaerobic fermentation. Supplementation with short-chain fatty acids, the primary fermentative products, restored normal VWR activity in microbiome-depleted mice. Conversely, 4-week dietary pretreatment with 2.5% prebiotic fiber (inulin) increased predicted fermentative capacity of the microbiota and VWR activity above baseline levels. Microbiome manipulation produced bidirectional dysregulation of corticosterone responses to exercise: acute antibiotic depletion increased post-exercise concentrations, while germ-free development decreased them, despite elevated striatal catecholamines. This exercise-specific uncoupling reveals microbiome-dependent integration of metabolic demand signals in the coordination of sympathetic and hypothalamic-pituitary-adrenal axis responses. Furthermore, the inulin-induced enhancement in VWR activity was associated with increased striatal histamine concentrations following exercise, suggesting additional mechanisms of neuromodulation. These findings demonstrate that the fermentative capacity of the gut microbiota influences exercise motivation and neuroendocrine regulation, providing novel insights into dietary interventions targeting physical activity.

IMPORTANCE: Physical inactivity is a leading cause of global morbidity and mortality, and our lack of understanding of the biological forces driving motivation to exercise limits our ability to develop interventions that enhance engagement. Using a rodent model of voluntary exercise along with microbiota depletion and metabolite replacement, we uncovered that the gut microbiota and its capacity to ferment dietary components into short-chain fatty acids drive exercise habit acquisition and help facilitate coordination between neurochemical signals and systemic stress hormones during exercise. Additionally, microbiome depletion "uncoupled" these systems, resulting in dysregulated stress responses during forced exercise. Finally, we showed that enhancement of microbiota fermentation capacity via dietary addition of prebiotic fiber was able to increase exercise engagement while also enhancing concentrations of histamine, a neuromodulator that potentiates locomotor activity, in the striatum. These findings suggest that the gut microbiome is a modifiable target for behavior change that facilitates integration of metabolic demand in neuroendocrine activity. Collectively, this work provides a mechanistic foundation to support the use of dietary interventions in sedentary populations to start exercise habits.},
}

Animals
*Motivation/physiology
Mice
Mice, Inbred C57BL
*Fermentation
*Gastrointestinal Microbiome/physiology/drug effects
Male
*Physical Conditioning, Animal/physiology
*Neurosecretory Systems/physiology/metabolism
Prebiotics
Corticosterone/blood
Fatty Acids, Volatile/metabolism

@article {pmid42635434,
year = {2026},
author = {Sakdinan, B and Sinha, A and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ},
title = {Species-specific prophage induction by ciprofloxacin in human gut metagenomes.},
journal = {mSystems},
volume = {11},
number = {9},
pages = {e0030326},
pmid = {42635434},
issn = {2379-5077},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; //McGill University Health Centre/ ; /NH/NIH HHS/United States ; },
mesh = {Humans ; *Prophages/drug effects/genetics ; *Ciprofloxacin/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Metagenome/drug effects ; *Virus Activation/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/virology/genetics ; Species Specificity ; Metagenomics ; },
abstract = {Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction, and whether it is associated with antibiotic exposure. In two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in certain bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut.IMPORTANCEBacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host cell to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death, which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro, whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations.},
}

Humans
*Prophages/drug effects/genetics
*Ciprofloxacin/pharmacology
*Gastrointestinal Microbiome/drug effects/genetics
*Metagenome/drug effects
*Virus Activation/drug effects
*Anti-Bacterial Agents/pharmacology
*Bacteria/drug effects/virology/genetics
Species Specificity
Metagenomics

@article {pmid42671180,
year = {2026},
author = {Li, T and Lu, X and Alomeir, N and Gaca, A and Sohn, M and Gill, S and Smith, B and Munger, J and Xiao, J},
title = {Longitudinal development of infant oral ecosystem: salivary metabolomic, bacteriome, and virome dynamics in early infancy.},
journal = {mSystems},
volume = {11},
number = {9},
pages = {e0094626},
pmid = {42671180},
issn = {2379-5077},
support = {R01 DE031025/DE/NIDCR NIH HHS/United States ; R01DE031025/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Saliva/microbiology/virology/metabolism ; Infant ; *Virome ; Female ; *Metabolome ; Longitudinal Studies ; Metabolomics/methods ; *Mouth/microbiology ; Male ; Child, Preschool ; Microbiota ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Prospective Studies ; Dental Plaque/microbiology/virology ; Multiomics ; },
abstract = {This prospective cohort study investigated the longitudinal development of the salivary bacteriome, virome, and metabolome during early infancy. We assessed the associations between oral bacteria, viruses, and metabolites from 10 mother-infant dyads, with oral samples collected at 1 and 2 years of age. Forty saliva and plaque samples underwent untargeted metabolomic analysis, and infant saliva samples underwent metagenomic sequencing. Maternal salivary and plaque metabolomic profiles remained largely stable, whereas infant profiles were clearly separated from maternal profiles and changed with age. Notably, infant dental plaque metabolism underwent more substantial changes from year 1 to year 2 than saliva, with age-dependent metabolite shifts mainly involving energy, amino acid, nucleotide, and lipid metabolic pathways. Our findings also revealed significant developmental shifts in salivary bacteriome, virome, and functional pathway profiles during early childhood. The most abundant oral bacteria in early life, comprising over 75% of total abundance, included Veillonella, Streptococcus, Rothia, Prevotella, Neisseria, and Actinomyces species. While human viruses like Roseolovirus were detected, bacteriophages constituted the majority of the virome. Comparing infants at year 1 and year 2, we identified differentially abundant bacteria, viruses, metabolic functional pathways, and specific metabolites. We observed associations between bacteria and viruses, noting that these cross-kingdom relationships attenuated as infants grew. The study results underscore the complex and dynamic development of the oral microbiome, virome, and metabolome during early childhood.IMPORTANCEThe human oral cavity undergoes substantial microbial and metabolic development during early childhood, yet the temporal changes in the infant oral ecosystem remain incompletely understood. In this study, we longitudinally profiled the salivary metabolome, bacteriome, and virome of infants at 1 and 2 years of age. We demonstrated that the infant oral metabolome undergoes substantial developmental shifts, particularly in pathways related to energy, amino acid, and lipid metabolism; whereas maternal metabolic profiles remained stable over the same period. Furthermore, our results revealed the dynamic assembly of infant salivary virome and bacteriome and their associations with the functional pathways and metabolites. These findings provide new insights into the complex and dynamic development of the oral microbiome, virome, and metabolome in early infancy.},
}

Humans
*Saliva/microbiology/virology/metabolism
Infant
*Virome
Female
*Metabolome
Longitudinal Studies
Metabolomics/methods
*Mouth/microbiology
Male
Child, Preschool
Microbiota
*Bacteria/genetics/classification/metabolism/isolation & purification
Prospective Studies
Dental Plaque/microbiology/virology
Multiomics

@article {pmid42678156,
year = {2026},
author = {Wu, Q-Q and Li, C-Y and Chen, S-S and Xu, J and Yan, W-H and Lu, L-N and Feng, H-X and Zhou, J-A and Wang, L and Liu, N-N and Jiang, L and Wang, Y},
title = {Multi-kingdom gut microbiota analyses identify biomarkers of different types of pediatric short bowel syndrome.},
journal = {mSystems},
volume = {11},
number = {9},
pages = {e0031626},
pmid = {42678156},
issn = {2379-5077},
support = {82370525//National Natural Science Foundation of China/ ; 2023YFC2706505//National Key R&D Program of China/ ; //Shanghai JiaoTong University School of Medicine "Double Hundred Talents" Program/ ; 82470602//National Natural Science Foundation of China/ ; 82570601//National Natural Science Foundation of China/ ; 23ZR1452600//Natural Science Foundation of Shanghai Municipality/ ; 22ZR1441100//Natural Science Foundation of Shanghai Municipality/ ; 2023005//Shanghai medical New Star Outstanding Young Medical Talents Project/ ; 20234Z0004//Shanghai Municipal Health Commission/ ; 2022YFA1305600//National Key R&D Program of China/ ; },
mesh = {Humans ; *Short Bowel Syndrome/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Child, Preschool ; Male ; Biomarkers ; Feces/microbiology ; Infant ; Bacteria/genetics/classification/isolation & purification ; Child ; Archaea/genetics/isolation & purification/classification ; },
abstract = {Despite recent advances in bacterial profiling across the three anatomical types of pediatric short bowel syndrome (SBS), the gut multi-kingdom remains unexplored. We characterized the four-kingdom gut microbiota using modified DNA extraction and deep shotgun metagenomic sequencing of fecal samples from 26 healthy controls and 34 pediatric SBS patients comprising three types (8 SBS I, 15 SBS II, and 11 SBS III). Overall, children with SBS exhibited a significant reduction in α-diversity compared with controls, with no difference observed among SBS types. Compared with controls, the proportion of archaea was significantly decreased in all SBS types, while bacteria, fungi, and viruses remained similar across types. Different types of SBS exhibited distinct microbial signatures: SBS I was enriched with pathogens (such as species from the Streptococcus and Klebsiella genera); SBS II was marked by a depletion of beneficial short-chain fatty acid-producing species (such as Faecalibacterium prausnitzii); and SBS III displayed loss of bile acid-metabolizing species, alongside a significant expansion of Lactobacillus species. Ecological networks were rewired in SBS, with disruption pronounced in SBS I. Functional analysis revealed that core metabolic pathways were markedly suppressed in SBS I compared with controls. Integrated correlation analyses revealed ileocecal valve loss as the primary determinant of SBS I microbial profiles, linking it to impaired secretory functions and hepatic injury. Our findings deciphered type-specific alterations in the multi-kingdom microbiota and their functional profiles, providing the basis for designing precision microbial therapies aimed at improving long-term outcomes for children with SBS.IMPORTANCEPediatric short bowel syndrome (SBS) is a primary cause of intestinal failure, yet prior research characterizing the gut microbiota has focused almost exclusively on bacteria. In this study, we characterized the multi-kingdom microbiome (including bacteria, fungi, archaea, and viruses) across the three anatomical types of pediatric SBS. We found that different SBS subtypes showed distinct microbial patterns: SBS I was enriched in pathogens, SBS II exhibited a depletion of beneficial short-chain fatty acid-producing species, and SBS III was characterized by a loss of bile acid-metabolizing microbes with an expansion of Lactobacillus. Functional analysis showed that SBS I had markedly suppressed core metabolic pathways, and integrated analyses identified the ileocecal valve as a key determinant of microbial gene profiles, with its loss linked to impaired secretion and liver injury. These findings provide a comprehensive multi-kingdom view of the pediatric SBS microbiome and highlight anatomical determinants shaping host-microbiome dysfunction.},
}

Humans
*Short Bowel Syndrome/microbiology
Female
*Gastrointestinal Microbiome/genetics
Child, Preschool
Male
Biomarkers
Feces/microbiology
Infant
Bacteria/genetics/classification/isolation & purification
Child
Archaea/genetics/isolation & purification/classification

@article {pmid42679417,
year = {2026},
author = {Li, H and Gao, H and Fu, J and Yang, S and Chen, L and Zhou, J},
title = {Comparative analysis of microbial communities, assembly processes, and life-history strategies in a mariculture-impacted eutrophic bay and adjacent coastal sediments.},
journal = {Ecotoxicology and environmental safety},
volume = {323},
number = {},
pages = {120750},
doi = {10.1016/j.ecoenv.2026.120750},
pmid = {42679417},
issn = {1090-2414},
mesh = {*Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bays/microbiology ; Eutrophication ; *Microbiota/drug effects ; China ; *Bacteria/genetics/classification/drug effects ; Metagenomics ; Seawater/microbiology ; Life History Traits ; },
abstract = {Coastal embayments are increasingly subjected to intensive mariculture, which delivers sustained nutrient, organic matter, and antibiotics to sediments, yet microbiome responses remain poorly understood. Here we compared sediment microbiomes of the eutrophic Xiangshan Bay (XSB) and oligotrophic East China Sea (ECS), integrating cell counts, 16S rRNA amplicon, metagenomics, and cultivation-based resistance assays. Cell counts and amplicon data showed that XSB harbored higher microbial abundance (1.28 ×10[8]-1.34 ×10[9] vs. 2.07 ×10[7]-4.43 ×10[8] cells g[-1]), Chao1 richness (10,374-16,674 vs. 8311-12,281), and Shannon diversity (6.31-7.43 vs. 5.95-6.68). Amplicon-based null and neutral models indicated that community assembly in XSB was less stochastic and more deterministically selected than in the ECS. Life-history traits inferred directly from metagenomic data were consistently elevated in XSB relative to ECS, including 16S rRNA gene copy number (3.35 vs. 2.37), codon usage bias (0.0219 vs. 0.0188), maximum growth potential (0.1208 vs. 0.0844 h[-1]), genome size (5.63 vs. 5.38 Mb), GC content (56.26% vs. 54.48%), and transposase abundance (3.91% vs. 2.55%), collectively indicating a transition from K- to r-selected life-history strategies. Moreover, metagenomic annotation revealed a similarly expanded resistome in XSB, with 4.5-fold higher antibiotic resistance gene abundance (17.40-45.37 vs. 7.96-25.96 RPM) dominated by efflux-pump mechanisms, while plate assays showed roughly two-fold higher phenotypic resistance to macrolides, tetracyclines, and sulfonamides. These findings demonstrate that microbial community, life-history strategies, and antibiotic resistance respond as a coupled system to mariculture-driven eutrophication, providing a trait-based framework for predicting microbiome trajectories under anthropogenic nutrient enrichment.},
}

*Geologic Sediments/microbiology
RNA, Ribosomal, 16S/genetics
*Bays/microbiology
Eutrophication
*Microbiota/drug effects
China
*Bacteria/genetics/classification/drug effects
Metagenomics
Seawater/microbiology
Life History Traits

@article {pmid42754330,
year = {2026},
author = {Na, SI and Kim, J and Kim, SY and Park, J and Cho, YJ},
title = {SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {9},
pages = {e2606011},
doi = {10.71150/jm.2606011},
pmid = {42754330},
issn = {1976-3794},
support = {//National Research Foundation of Korea/ ; RS-2023-00301850//Ministry of Education/ ; RS-2026-25491179//Ministry of Science and ICT/ ; 2024ER210600//Korea National Institute of Health research project/ ; },
mesh = {*Microbiota ; Internet ; *Software ; Bacteria/classification/genetics ; *Computational Biology/methods ; Workflow ; Metagenomics/methods ; },
abstract = {Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image. SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.},
}

*Microbiota
Internet
*Software
Bacteria/classification/genetics
*Computational Biology/methods
Workflow
Metagenomics/methods

@article {pmid42765765,
year = {2026},
author = {Benot, AO and Waldschmidt, G and Gilvarg, SC and Legge, EOL and Okyere, IJ and Tiyapun, C and Lucas, SK and Vander Yacht, AL and Goff, JL},
title = {Prescribed burns drive lasting changes in soil nitrogen cycling and microbial function.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0085226},
doi = {10.1128/msystems.00852-26},
pmid = {42765765},
issn = {2379-5077},
abstract = {Fire is a major pulse disturbance to soil microbial communities, with broad implications for nutrient cycling; however, regular burning is also a natural and often-essential process maintaining biodiversity in unique and imperiled fire-dependent ecosystems. Prescribed fire is widely used to promote this biodiversity and simultaneously reduce wildfire risk. Although such repeated burning is known to alter surface biodiversity, belowground soil geochemistry, and soil microbial community structure, the functional consequences (i.e., the metabolic capabilities that underlie the ecosystem services soil microorganisms provide) remain underexplored. Here, we examined the effects of 30 years of repeated prescribed fire at the Albany Pine Bush-a fire-dependent, inland pitch pine barren ecosystem of the northeastern United States. Compared with the control stands, we observed that this long-term fire management has led to substantial depletion of inorganic soil nitrogen, specifically nitrate. We found no meaningful differences in the higher-level taxonomic composition of soil prokaryotic or fungal communities; however, analysis of metagenome-assembled genomes assembled from these soils revealed several differentially abundant populations. Furthermore, our metagenomic analysis revealed significant changes in the nitrogen-cycling functional potential, specifically decreased dissimilatory nitrate reduction and denitrification potential in repeatedly burned soils. These functional shifts have important implications for both nutrient cycling and emissions of trace nitrogen gases from these soils. Our results suggest that functionally meaningful changes in the soil microbiome can persist between burn events, even when higher-order community membership appears stable. This may imply that repeated fire can deplete reactive nitrogen emissions from soils by lowering the functional capacity of nitrogen-reducing microbes.IMPORTANCEPrescribed fire is widely used by land managers to reduce wildfire risk and promote biodiversity. While the effects of fire on aboveground processes are well understood, much less is known about how repeated burning influences soil biological properties-including the functional role that soil microorganisms play in nutrient cycling and greenhouse gas production. We addressed this gap by studying soils from the Albany Pine Bush, a rare and endangered ecosystem that has experienced regular prescribed fires for 30 years. Long-term fire management significantly altered soil chemistry, specifically lowering the amount of nitrogen in the soil. In addition, we found that fire management decreased the genetic potential of the soil microbial community to produce nitrogen oxides-potent contributors to climate change. Thus, prescribed fire's contribution to greenhouse gas emissions may involve a complex relationship between direct fire-driven emissions, increased fire resilience of promoted vegetation, and-as suggested by our results-the reduced ability of soil microbes to produce greenhouse gases.},
}

@article {pmid42767975,
year = {2026},
author = {Burge, K and Velsko, IM and Salazar-García, DC and Uriarte, MH and Lomba Maurandi, J and Warinner, C},
title = {Comparing the Performance of Double-Stranded and Single-Stranded DNA Libraries for Ancient Oral Microbiome Reconstruction.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70201},
pmid = {42767975},
issn = {1755-0998},
support = {//Werner Siemens-Stiftung/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; //National Science Foundation/ ; },
mesh = {Animals ; *Microbiota ; *Mouth/microbiology ; *Gene Library ; Humans ; *DNA, Ancient ; Sequence Analysis, DNA ; DNA, Single-Stranded/genetics ; Neanderthals ; *Metagenomics/methods ; },
abstract = {DNA library construction methods can affect the recovery of ancient DNA, thus influencing downstream analyses. While single-stranded library preparation (ssLib) has been shown to outperform double-stranded (dsLib) for highly degraded vertebrate host DNA, especially for samples older than 40,000 years, few studies have examined how library protocols shape ancient microbial community reconstruction. Here, we compare the sequencing output of paired ssLib and dsLib dental calculus libraries generated from 12 Neanderthals and two Chalcolithic humans, prepared using implementations of the Gansauge et al. and Meyer and Kircher protocols, respectively, and sequenced with identical Illumina chemistry. We compared read length and GC%, read duplication and taxonomic profiles across normalization strategies to assess protocol-specific biases. Double-stranded libraries retained a significantly higher proportion of sequenced reads throughout data processing (dsLib 72.1%, ssLib 37.9%), a higher proportion of oral reads (dsLib 9.78%, ssLib 6.75%), significantly longer median oral DNA read lengths (dsLib 57.5 bp, ssLib 50.5 bp) and more GC-rich fragments (dsLib 60.5% GC, ssLib 52.5% GC). In contrast, ssLibs exhibited slightly higher Shannon diversity and a greater proportion of unique reads. Despite these differences, species richness and overall community composition was not significantly different between protocols, with individual and preservation status explaining the most variance. Stratifying reads by length (< 50 bp vs. ≥ 50 bp) resulted in different classification rates but only had minor effects on diversity estimates. Together, these results demonstrate that dsLib and ssLib protocols impose distinct trade-offs and library choice should be guided by study-specific goals.},
}

Animals
*Microbiota
*Mouth/microbiology
*Gene Library
Humans
*DNA, Ancient
Sequence Analysis, DNA
DNA, Single-Stranded/genetics
Neanderthals
*Metagenomics/methods

@article {pmid42768305,
year = {2026},
author = {Avershina, E and Birkeland, EE and Bucher-Johannessen, C and Rounge, TB},
title = {CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2734649},
pmid = {42768305},
issn = {1949-0984},
mesh = {Humans ; *Interspersed Repetitive Sequences ; *Bacteria/genetics/classification/immunology/isolation & purification/virology ; *Gastrointestinal Microbiome/genetics ; *CRISPR-Cas Systems ; Plasmids/genetics ; Feces/microbiology ; Middle Aged ; Metagenome ; Norway ; Female ; Diet ; Bacteriophages/genetics ; Gastrointestinal Tract/microbiology ; },
abstract = {Bacteria in the human gut influence host physiology and disease risk, but their ecology is strongly shaped by mobile genetic elements (MGEs) such as phages and plasmids. Past interactions between bacteria and MGEs can be inferred from CRISPR-Cas cassettes, which contain short DNA fragments derived from invading elements. To lay the groundwork for research on the impact of such interactions on the human host, we constructed an extended microbiome resource comprising 1.7 K prokaryotic mOTUs, 19.5 K viral vOTUs, and 24.2 K plasmid PTUs, using fecal shotgun metagenomes from 1034 adults over 55 y of age residing in South-East Norway. We also recovered 74.2 K unique CRISPR-Cas cassettes to map past bacteria-MGE interactions and assessed their associations with the human diet and lifestyle factors. CRISPR-Cas spacers, and which viruses and plasmids they targeted, varied substantially within bacterial species, but were predominantly directed towards cohort-specific MGEs. Moreover, bacteria were more likely to target MGEs present in the same sample, consistent with local exposure. Plasmid MGEs were more often targeted by Type II CRISPR-Cas cassettes, whereas viruses were more likely to be targeted by Type I CRISPR-Cas cassettes. Bacteria also shared more targets within taxonomic families than across families, where mobilizable plasmids were more frequent among the targets. CRISPR-Cas cassettes mirrored microbiome associations to human demographic and lifestyle factors and enabled the recovery of dairy-associated B. animalis. Together, this research provides a large-scale resource and a structured analysis of bacteria-MGE interactions in the gut microbiome and their contribution to microbial ecosystem dynamics.},
}

Humans
*Interspersed Repetitive Sequences
*Bacteria/genetics/classification/immunology/isolation & purification/virology
*Gastrointestinal Microbiome/genetics
*CRISPR-Cas Systems
Plasmids/genetics
Feces/microbiology
Middle Aged
Metagenome
Norway
Female
Diet
Bacteriophages/genetics
Gastrointestinal Tract/microbiology

@article {pmid42771532,
year = {2026},
author = {Igwe, AN and Afkhami, ME},
title = {Redundancy maintains microbial ecosystem functional potential despite taxonomic shifts between serpentine and nonserpentine soils.},
journal = {Microbial genomics},
volume = {12},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001835},
pmid = {42771532},
issn = {2057-5858},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Bacteria/classification/genetics/isolation & purification ; Archaea/classification/genetics/isolation & purification ; California ; *Microbiota/genetics ; *Fungi/classification/genetics/isolation & purification ; Metagenomics/methods ; Ecosystem ; Metagenome ; },
abstract = {Environmental filtering and buffering are complementary processes responsible for stabilizing ecosystem services across landscapes. The extent to which either of these processes structures microbial composition and functions in extreme soil systems can be highly context-dependent, requiring site-specific examination to elucidate general principles of community function under stress. Serpentine soils have high amounts of heavy metals and magnesium and low levels of plant nutrients and exist in close proximity to nutrient-rich and plant-productive nonserpentine soils, making them an ideal system for evaluating selection and redundancy under stress. Combining biogeographical field surveys and shotgun metagenomic sequencing of microbiomes from 23 pairs of serpentine and nonserpentine soils across California, we investigated selection and functional redundancy between disparate soil types. We hypothesized that the strong selective pressure present in serpentine soils would result in distinct bacterial and functional profiles. Bacterial and fungal community taxonomic compositions were indeed distinct between serpentine and nonserpentine soils, while archaeal communities were similar between soil types. In contrast, functional repertoires of all microbial community groups were largely similar between soil types, with many of the same taxa carrying out functions across soil types. Still specialized functions in serpentine soils represented adaptations to stress in contrast to the carbon-rich environment of nonserpentine soils. For example, specialized functions - such as siderophore biosynthesis proteins, which are involved in the biosynthesis of iron-chelating compounds - were distinctive features of serpentine soils and specialized functions notably had similar functional redundancy but distinct taxa carrying out the functions across soil types. These results highlight taxa that perform the functions that have been selected for survival in an extreme soil ecosystem and the functions that are most at risk in the face of environmental disturbances.},
}

*Soil Microbiology
*Soil/chemistry
*Bacteria/classification/genetics/isolation & purification
Archaea/classification/genetics/isolation & purification
California
*Microbiota/genetics
*Fungi/classification/genetics/isolation & purification
Metagenomics/methods
Ecosystem
Metagenome

@article {pmid42555106,
year = {2026},
author = {Luo, Z and Liu, Y and Wu, H and Xiao, Y and Li, Y and Liu, M and Li, C and Zhu, D and Jin, LN and Dong, T and Yan, W},
title = {Zoo gut plastispheres enable pathogen escape and adaptation.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag207},
pmid = {42555106},
issn = {1751-7370},
support = {22425041//National Natural Science Foundation of China/ ; 22188102//National Natural Science Foundation of China/ ; 2023JJ30986//National Natural Science Foundation of China/ ; 2024JJ1016//National Natural Science Foundation of China/ ; 2022RC1118//Science and Technology Innovation Program of Hunan Province/ ; GZC20242059//Postdoctoral Science Foundation/ ; XLKJ202303//Scientific Research Project of Hunan Provincial Department of Education/ ; P0040336//Scientific Research Project of Hunan Provincial Department of Education/ ; },
mesh = {Animals ; Feces/microbiology/chemistry ; *Animals, Zoo/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Microplastics/analysis ; *Gastrointestinal Microbiome ; Humans ; Biofilms ; Metagenomics ; Adaptation, Physiological ; },
abstract = {In zoos, intensive human contact and artificial feeding may create pathways for microplastic (MP) ingestion and gut colonization. We hypothesized that ingested MPs form intestinal plastispheres with elevated pathogenic potential and enhanced environmental persistence. To test this, we surveyed feces from 15 zoo-dwelling species and coupled particle characterization, feces-derived intestinal simulations, metagenomic sequencing, and a subsequent water-exposure experiment. Zoo feces contained more abundant MPs than reported for wild counterparts, with fragments predominating and polyethylene terephthalate (PET)/polystyrene (PS) dominating polymer profiles. MP burdens tracked human-animal interaction patterns, with human-fed species (e.g. Tiger, Elephant) carrying the highest loads (88-212 items/g). MPs supported dense biofilms whose composition diverged from bulk gut communities, exhibiting greater compositional variability and substrate-specific assembly. Metagenomic analyses revealed coordinated enrichment of potentially pathogenic taxa, virulence factor genes (VFGs), and antibiotic resistance genes (ARGs), with ARG profiles dominated by efflux- and inactivation-related mechanisms and tightly associated with mobile genetic elements. Elevated Type II/III/IV/VI secretion systems and effector delivery-related VFGs occurred within extracellular polymeric substance-rich biofilms, suggesting enhanced potential for ARG retention and horizontal gene transfer. During the 35-day aquatic exposure, MP-associated communities persisted longer than non-plastic particle-associated communities and free gut microbiota, suggesting that plastic-specific properties promote microbial persistence. PET/PS plastispheres showed the slowest declines in bacterial activity and favored the persistence of Enterococcus, Enterobacter, and Clostridium. Overall, intestinal MPs in zoo animals may select, enrich, and export high-risk microbiomes, highlighting the need for MP mitigation and evidence-based management of zoos and adjacent ecosystems.},
}

Animals
Feces/microbiology/chemistry
*Animals, Zoo/microbiology
*Bacteria/genetics/classification/isolation & purification
*Microplastics/analysis
*Gastrointestinal Microbiome
Humans
Biofilms
Metagenomics
Adaptation, Physiological

@article {pmid42657522,
year = {2026},
author = {Zheng, Y and Zhuang, H and Dan, L and Zhou, Y and Yan, B and Zhang, Y and Zou, D and Wang, X and Sun, J},
title = {Resistant starch alleviates intestinal fibrosis involving an acetate-mediated HDAC2-H3K27ac axis in fibroblasts.},
journal = {Food & function},
volume = {17},
number = {18},
pages = {8215-8230},
doi = {10.1039/d6fo01179a},
pmid = {42657522},
issn = {2042-650X},
mesh = {Animals ; Mice ; *Starch/pharmacology/metabolism ; *Fibroblasts/metabolism/drug effects ; Humans ; *Histones/metabolism ; Male ; Fibrosis ; Mice, Inbred C57BL ; *Histone Deacetylase 2/metabolism/genetics ; *Acetates/metabolism ; Colitis/chemically induced/metabolism ; *Intestines/pathology ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Dextran Sulfate ; },
abstract = {Dietary fibre-based interventions are of growing interest for the prevention and treatment of digestive diseases. In this study, we investigated the effect of resistant starch (RS) on intestinal fibrosis, a stricturing condition driven by excessive extracellular matrix (ECM) accumulation. RS was found to alleviate intestinal fibrosis in a dextran sulfate sodium (DSS)-induced chronic colitis mouse model, as evidenced by restored colon length, reduced ECM deposition (fibronectin and collagen I), and decreased levels of α-smooth muscle actin. Given that RS is fermented by the gut microbiota in the colon, metagenomic sequencing revealed that RS reshaped the composition of the gut microbiota and increased the abundance of beneficial gut bacteria, including Bacteroides acidifaciens, Faecalibaculum rodentium, and Bifidobacterium pseudolongum, which are known to enhance the production of short-chain fatty acids. Targeted metabolomic analysis further showed a marked increase in acetate levels, which was associated with reduced intestinal fibrosis. However, direct in vivo evidence that acetate is required for the anti-fibrotic effect of RS remains lacking. Using human (CCD-18Co) and primary mouse intestinal fibroblasts, the major ECM-producing cells that drive fibrosis progression, we demonstrated that acetate inhibited TGF-β-induced fibroblast activation by inhibiting histone deacetylase 2, thereby enhancing the acetylation level of histone H3 at lysine 27. Collectively, these results suggest a potential microbial-metabolic-epigenetic axis linking RS and acetate to fibrosis attenuation, which awaits causal validation in vivo. This axis holds promise as a therapeutic target for fibrotic diseases.},
}

Animals
Mice
*Starch/pharmacology/metabolism
*Fibroblasts/metabolism/drug effects
Humans
*Histones/metabolism
Male
Fibrosis
Mice, Inbred C57BL
*Histone Deacetylase 2/metabolism/genetics
*Acetates/metabolism
Colitis/chemically induced/metabolism
*Intestines/pathology
Gastrointestinal Microbiome/drug effects
Disease Models, Animal
Dextran Sulfate

@article {pmid42762131,
year = {2026},
author = {Xiang, Q and Li, Y and Yang, J},
title = {Translational efficiency guides microbial community remodeling.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2736907},
doi = {10.1080/19490976.2026.2736907},
pmid = {42762131},
issn = {1949-0984},
mesh = {*Microbiota ; Metagenomics ; *Microbial Interactions ; *Bacteria/genetics/metabolism ; *Protein Biosynthesis ; },
abstract = {While metagenomics provides compositional insights, its correlative nature limits causal community remodeling. Overcoming this, in a recent Cell study, Moyne et al. introduced the Microbial Interaction and Niche Determination (MIND) framework. By leveraging translational efficiency to map resource competition and niche partitioning, MIND establishes a mechanistic blueprint for rational engineering.},
}

*Microbiota
Metagenomics
*Microbial Interactions
*Bacteria/genetics/metabolism
*Protein Biosynthesis

@article {pmid42764218,
year = {2026},
author = {Huang, QY and Xiang, HR and Tu, HK},
title = {[Current research status of the intratumoral microbiome and evolution of detection technologies].},
journal = {Zhonghua zhong liu za zhi [Chinese journal of oncology]},
volume = {48},
number = {9},
pages = {1124-1138},
doi = {10.3760/cma.j.cn112152-20260303-00105},
pmid = {42764218},
issn = {0253-3766},
support = {82574197//National Natural Science Foundation of China/ ; K20230085//Healthy Zhejiang One Million People Cohort/ ; },
mesh = {Humans ; *Microbiota ; *Tumor Microenvironment ; *Neoplasms/microbiology/pathology ; Metagenomics ; Bacteria/isolation & purification ; },
abstract = {As a core functional component of the tumor microenvironment, the regulatory role of intratumoral microbiome in tumorigenesis and progression has become as a frontier research direction in oncology. Microorganisms such as bacteria, fungi, and viruses participate in the regulation of tumor biological mechanisms through multiple pathways, including metabolite secretion, induction of genomic instability, and remodeling of the immune microenvironment; their species composition and abundance characteristics exhibit distinct cancer-type specificity, and their impact on patient prognosis is highly context-dependent. Current detection systems for the intratumoral microbiome mainly encompass in situ detection technologies, metagenomic sequencing, and computational pathology-driven intelligent detection, each with its own advantages and limitations, among which intelligent detection centered on deep learning is gradually overcoming the technical bottlenecks of identifying low-abundance microbial signals, achieving accurate quantification, and resolving spatial distribution. In the future, with the deep integration of three-dimensional pathological imaging, spatial omics, and multi-modal foundation models, intratumoral microbiome research will advance toward the in-depth development of multi-dimensional data integration, providing innovative ideas and technical pathways for elucidating the regulatory mechanisms between microorganisms and the host and for developing precision diagnostic and treatment strategies based on individual microecological characteristics.},
}

Humans
*Microbiota
*Tumor Microenvironment
*Neoplasms/microbiology/pathology
Metagenomics
Bacteria/isolation & purification

@article {pmid42765266,
year = {2026},
author = {Wang, DD and Xie, YQ and Huang, YF and Jia, HC},
title = {[Seasonal Response Features of Microbial Community Structure for Nitrogen Transformation in Inland Lakes on the Qinghai-Xizang Plateau].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {9},
pages = {6558-6568},
doi = {10.13227/j.hjkx.202507365},
pmid = {42765266},
issn = {0250-3301},
mesh = {*Lakes/microbiology/chemistry ; *Nitrogen/metabolism/isolation & purification ; Seasons ; China ; *Bacteria/metabolism/classification ; *Water Microbiology ; Ecosystem ; *Microbiota ; },
abstract = {Studying the nitrogen transformation characteristics of microbial communities in the inland lakes of the Qinghai-Xizang Plateau （QXP） is of great significance for a deeper understanding of the nitrogen budget balance and biogeochemical cycling in the regional lake ecosystems. Based on metagenomic sequencing technology， this study constructed a non-redundant gene library of nitrogen-transforming microorganisms and conducted multivariate statistical analysis to explore the characteristics and assembly mechanisms of nitrogen-transforming microbial communities in inland lakes on the QXP. The results indicate： ① Bacteria were the main group of nitrogen transformation microbes in the plateau inland lakes. The dominant bacterial phylum involved in nitrogen conversion both in summer and winter was Pseudomonadota， with an average proportion of 39.35% and 35.09% at different sampling sites in different seasons， respectively. The dominant bacterial genera in summer and winter were Candida_planktophila （the average proportion of different sampling sites was 4.04%） and unclassified_c_Actinomycetes （the average proportion of different sampling sites was 7.91%）. ② Salinity and dissolved oxygen were the most significant environmental factors affecting the microbial community structure of nitrogen transformation in different seasons. There were differences in the process of nitrogen transformation microbial community assembly in different seasons and different sampling lakes. ③ There were differences in the abundance of functional genes of nitrogen transformation microbes in different seasons， and denitrification was the most widely involved process of microbial communities in the plateau inland lakes in different seasons. The environmental factors driving the abundance of nitrogen transformation genes in different seasons were altitude， water temperature， total dissolved solids， and salinity. Overall， there was significant spatiotemporal heterogeneity in the assembly process of nitrogen transformation microbial communities in the plateau inland lakes. The results of this study can provide data support for the understanding of nitrogen-transforming microbes in the plateau inland lake ecosystem and provide a theoretical basis for lake water ecological management and regional greenhouse gas emissions.},
}

*Lakes/microbiology/chemistry
*Nitrogen/metabolism/isolation & purification
Seasons
China
*Bacteria/metabolism/classification
*Water Microbiology
Ecosystem
*Microbiota

@article {pmid42761166,
year = {2026},
author = {Li, M and Zhao, X and Zhang, B and Cao, R and Wang, Z and Huang, Z and Cheng, C and Lu, S and Jiang, X},
title = {Gut microbiome-metabolome signatures of osteosarcopenia in fracture patients in China.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1863988},
pmid = {42761166},
issn = {1664-2392},
mesh = {Humans ; Female ; Male ; Middle Aged ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Prospective Studies ; *Fractures, Bone/metabolism/microbiology/complications/epidemiology ; Aged ; China/epidemiology ; *Metabolome ; *Sarcopenia/microbiology/metabolism/epidemiology ; Multiomics ; Metabolomics ; Metagenomics ; },
abstract = {BACKGROUND: Osteosarcopenia, defined as the coexistence of low bone mass and sarcopenia, is a disabling musculoskeletal condition, yet its gut microbial and metabolic characteristics in clinical populations remain incompletely understood. Integrative multi-omics approaches may help clarify species-metabolite networks associated with this condition, particularly in fracture patients.

METHODS: In this single-center, prospective cross-sectional study, 69 fracture patients aged ≥50 years were classified into four phenotypes: Normal (n = 18), isolated low bone mass (Bone, n = 18), isolated sarcopenia (Muscle, n = 19), and osteosarcopenia (Both, n = 14). Fecal samples were analyzed using shotgun metagenomics and untargeted metabolomics, yielding paired multi-omics data for 52 participants.

RESULTS: The Bone group had the highest mean age (66.6 ± 9.46 years), whereas the mean ages of the other groups ranged from 60.6 to 61.8 years (overall p = 0.029), while sex, BMI, lifestyle factors, and comorbidities did not differ significantly. Neither α-diversity nor overall β-diversity showed marked differences across phenotypes, suggesting that broad community replacement was not observed. A multi-stage, multi-method strategy yielded a 17-species consensus feature set associated with differences among musculoskeletal phenotypes. Taxonomic patterns were consistent with a candidate fiber/short-chain fatty acid (SCFA)-associated module, whereas exploratory microbe-metabolite correlations suggested a candidate lipid/sterol-associated module. The latter included correlations linking Firmicutes bacterium CAG:24053_14 with putatively annotated cholesterol and N-acylethanolamines.

CONCLUSIONS: Osteosarcopenia in fracture patients was associated with unadjusted differences in selected gut microbial taxa and fecal metabolites within a broadly shared microbial community. These findings are hypothesis-generating and require validation in larger independent cohorts before clinical or biomarker application.},
}

Humans
Female
Male
Middle Aged
Cross-Sectional Studies
*Gastrointestinal Microbiome
Prospective Studies
*Fractures, Bone/metabolism/microbiology/complications/epidemiology
Aged
China/epidemiology
*Metabolome
*Sarcopenia/microbiology/metabolism/epidemiology
Multiomics
Metabolomics
Metagenomics

@article {pmid42669226,
year = {2026},
author = {Gongpan, P and Yang, J and Fu, H and Wu, S and Zhu, X and Chen, R and Liu, L and Geng, CA},
title = {Preparation and chemical characterization of polyphenol-rich extract from Tsaoko Fructus: alleviation of ulcerative colitis in mice by modulating gut microbiota and suppressing the JNK1-cJun signaling.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {161},
number = {},
pages = {158752},
doi = {10.1016/j.phymed.2026.158752},
pmid = {42669226},
issn = {1618-095X},
mesh = {Animals ; *Colitis, Ulcerative/drug therapy/microbiology/chemically induced ; *Polyphenols/pharmacology/chemistry ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/pharmacology/chemistry ; Male ; *Anti-Inflammatory Agents/pharmacology ; Disease Models, Animal ; Dextran Sulfate ; Signal Transduction/drug effects ; *Mitogen-Activated Protein Kinase 8/metabolism ; Mice, Inbred C57BL ; Colon/drug effects ; Molecular Docking Simulation ; },
abstract = {BACKGROUND: Tsaoko Fructus, a traditional Chinese medicinal herb, has long been used to alleviate gastritis and enteritis. Nevertheless, the active constituents and underlying anti-inflammatory mechanisms remain insufficiently characterized.

PURPOSE: This study aims to optimize a polyphenol-rich fraction (3CB) from Tsaoko Fructus, evaluate its effects against ulcerative colitis (UC), and reveal the underlying mechanisms of action.

METHODS: The preparation of 3CB was optimized using response surface methodology (RSM), and its major constituents were identified by LC-PDA-MS analysis. A murine UC model was established by administering dextran sulfate sodium (DSS). To evaluate the effects of 3CB on UC mice, metagenomic sequencing of the intestinal microbiome and RNA sequencing of colon tissues were conducted. The anti-inflammatory activity of 3CB and its principal constituents was further verified by quantitative real-time PCR (qPCR), Enzyme linked immunosorbent assay (ELISA), Western blotting, immunohistochemical staining, and histopathological analysis. Network pharmacology, molecular docking, and surface plasmon resonance (SPR) assays were employed to elucidate the molecular mechanisms underlying the anti-inflammatory effects of 3CB.

RESULTS: 3CB significantly alleviated UC symptoms in DSS-induced mice, reshaped the gut microbiota with reducing pathogenic Pseudomonadota and Deferribacterota while enriching beneficial Bacteroidota, and restored microbial amino sugar and nucleotide sugar metabolism pathways of intestinal flora. Additionally, 3CB preserved colonic oxidative phosphorylation, protected the mucus barrier, and suppressed inflammatory cell infiltration and the expression of cytokines. Seven major polyphenols were identified in 3CB, with epicatechin (3) and epiafzelechin (6) being the most abundant. Mechanistic investigation revealed that the anti-inflammatory effect of 3CB was partially dependent on the JNK1-modulated MAPK signaling pathway. JNK1 was identified as a direct target of 3CB, with epiafzelechin (6) exhibiting a high binding affinity (Kd = 10.4 μM).

CONCLUSION: 3CB ameliorates UC potentially through modulation of gut microbiota, protection of the mucus barrier, and JNK1-targeted anti-inflammatory effects, highlighting its potential as a protective intervention for inflammatory bowel disease (IBD).},
}

Animals
*Colitis, Ulcerative/drug therapy/microbiology/chemically induced
*Polyphenols/pharmacology/chemistry
*Gastrointestinal Microbiome/drug effects
Mice
*Drugs, Chinese Herbal/pharmacology/chemistry
Male
*Anti-Inflammatory Agents/pharmacology
Disease Models, Animal
Dextran Sulfate
Signal Transduction/drug effects
*Mitogen-Activated Protein Kinase 8/metabolism
Mice, Inbred C57BL
Colon/drug effects
Molecular Docking Simulation

@article {pmid42697040,
year = {2026},
author = {Frangieh, MR and Saad, M and Fattouh, N and Sawan, S},
title = {Antibiotics and nanoparticles in Parkinson's disease: From gut microbiota dysbiosis to neuroprotection and targeted nanotherapies.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {203},
number = {},
pages = {119903},
doi = {10.1016/j.biopha.2026.119903},
pmid = {42697040},
issn = {1950-6007},
mesh = {Humans ; Animals ; *Anti-Bacterial Agents/adverse effects/administration & dosage/therapeutic use/pharmacology ; *Parkinson Disease/drug therapy/microbiology ; *Dysbiosis/drug therapy ; *Neuroprotective Agents/administration & dosage/therapeutic use/adverse effects ; *Nanoparticles ; *Gastrointestinal Microbiome/drug effects/physiology ; *Neuroprotection/drug effects ; Nanoparticle Drug Delivery System ; Nanomedicine/methods ; },
abstract = {Parkinson's disease (PD) is increasingly linked to gut-brain axis dysfunction. While broad-spectrum antibiotics may contribute to gut dysbiosis, which has been associated with an increased abundance of curli-producing Enterobacteriaceae and processes implicated in α-synuclein aggregation, certain antibiotic classes, particularly tetracyclines and β-lactams, have demonstrated neuroprotective properties in pre-clinical models of PD. This creates a therapeutic paradox: antibiotics may exert either beneficial or detrimental effects depending on many factors including host microbiome composition. Importantly, much of the current evidence remains observational or pre-clinical, and a direct causal relationship between antibiotic exposure and PD has not yet been established. This review synthesizes current epidemiological, mechanistic, and pre-clinical evidence regarding this paradox and explores the emerging role of nanotechnology in resolving it. Preclinical studies suggest that nanoparticle-based drug delivery systems may enhance BBB penetration and enable more targeted drug release. Such approaches have been proposed as a means to reduce systemic exposure and potentially limit microbiota disruption, although these benefits have not yet been demonstrated in clinical PD populations. We further discuss the translational hurdles, including nanotoxicity and regulatory requirements, and propose a roadmap for future research that integrates metagenomics with precision nanomedicine. Collectively, these findings provide a framework for future investigation of targeted therapeutic strategies for PD. However, substantial mechanistic, clinical, and translational validation is required before their therapeutic potential can be established.},
}

Humans
Animals
*Anti-Bacterial Agents/adverse effects/administration & dosage/therapeutic use/pharmacology
*Parkinson Disease/drug therapy/microbiology
*Dysbiosis/drug therapy
*Neuroprotective Agents/administration & dosage/therapeutic use/adverse effects
*Nanoparticles
*Gastrointestinal Microbiome/drug effects/physiology
*Neuroprotection/drug effects
Nanoparticle Drug Delivery System
Nanomedicine/methods

@article {pmid42758711,
year = {2026},
author = {Emfietzoglou, M and Bantounou, MA and Osmani, S and Narimatsu, T and Baroutis, KG and Varsamidaki, A and Skondra, D and Papaconstantinou, D and Theodossiadis, P and Chatziralli, I and Miller, JW and Vavvas, DG},
title = {Shotgun metagenomic profiling of the fecal microbiome in Lamp2 knockout mice reveals limited genotype-associated differences under standard housing.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357009},
doi = {10.1371/journal.pone.0357009},
pmid = {42758711},
issn = {1932-6203},
mesh = {Animals ; *Feces/microbiology ; Mice ; Male ; Mice, Knockout ; *Metagenomics/methods ; *Lysosomal-Associated Membrane Protein 2/genetics ; Genotype ; *Gastrointestinal Microbiome/genetics ; Shotgun Sequencing ; Metagenome ; },
abstract = {BACKGROUND: Lysosomal pathways influence host-microbe interactions, but the microbiome consequences of lysosomal dysfunction remain incompletely defined. LAMP2 is required for autophagosome-lysosome fusion, and pathogenic variants in LAMP2 cause Danon disease. Whether Lamp2 loss alters the gut microbiome in vivo has not been systematically evaluated using methods that profile both taxonomic composition and microbial functional potential, such as shotgun metagenomics.

METHODS: We performed shotgun metagenomic sequencing on 50 fecal samples from male Lamp2 knockout (Lamp2KO) mice and wild-type (WT) littermates sampled at 3, 6, 9, and 12 months under single-genotype cages or mixed-genotype cohousing. Two low-depth libraries (<3 × 105 classified genus-level reads) were excluded from primary inference (primary set: n = 48). We analyzed genus-level alpha diversity, beta diversity, and differential abundance using compositional, cage-aware mixed-effects models and cage-blocked permutation testing. We analyzed functional pathway profiles using copies-per-million abundances with centered-log-ratio transformation and mixed-effects modeling. We controlled multiple testing using the Benjamini-Hochberg false discovery rate.

RESULTS: In the primary set (48 samples from 27 cages), Lamp2KO and WT mice showed similar genus-level alpha diversity and overall community composition (PERMANOVA using Aitchison and Bray-Curtis distances). Primary mixed-effects models detected no genera with differential abundance after false discovery rate correction. Taxonomic profiles were broadly similar between genotypes and were dominated by Bacteroidota and Bacillota. Exploratory within-cage (paired) analyses identified consistent directional differences in a small set of genera, but these signals were not supported by the primary mixed-effects models. Functional pathway profiles were similar between genotypes; one pathway (dTDP-β-L-rhamnose biosynthesis) showed an exploratory association (FDR q < 0.10) within the 50 most abundant pathways.

CONCLUSIONS: In this controlled mouse cohort, we did not detect robust, cage-independent shifts in fecal microbiome composition or inferred functional pathway profiles associated with Lamp2 deficiency under standard SPF husbandry and chow; given the sample size, smaller or compartment-specific effects cannot be excluded.},
}

Animals
*Feces/microbiology
Mice
Male
Mice, Knockout
*Metagenomics/methods
*Lysosomal-Associated Membrane Protein 2/genetics
Genotype
*Gastrointestinal Microbiome/genetics
Shotgun Sequencing
Metagenome

@article {pmid42760068,
year = {2026},
author = {Toufiq, R and Shahid, A and Zahra, R and Lankapalli, AK and Oduwo, J and Owinoh, EO and Aftab, S and Hassan, B and Thomson, K and Walsh, TR and Sands, K},
title = {Cohort profile: Infant Gut Bacterial Study in Pakistan (INBUGS-P) longitudinal birth cohort.},
journal = {BMJ open},
volume = {16},
number = {9},
pages = {e120775},
doi = {10.1136/bmjopen-2026-120775},
pmid = {42760068},
issn = {2044-6055},
mesh = {Humans ; Pakistan ; Female ; Infant ; Longitudinal Studies ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Breast Feeding/statistics & numerical data ; Anti-Bacterial Agents/therapeutic use ; Birth Cohort ; Adult ; Milk, Human/microbiology ; },
abstract = {PURPOSE: The Infant Gut Bacterial Study in Pakistan (INBUGS-P) was established to characterise the longitudinal development of the infant gut microbiome and resistome during the first year of life in a low- and middle-income country setting. The influence of early-life exposures, including mode of delivery, antibiotic use and infant feeding practices on gut bacterial diversity and antimicrobial resistance gene (ARG) profiles is being evaluated.

PARTICIPANTS: A total of 107 mother-infant pairs were recruited at the Pakistan Institute of Medical Sciences between December 2023 and June 2024. Follow-up was conducted at 10 predefined timepoints from birth to 12 months, during which 921 infant stool samples, 158 maternal rectal swabs, 246 breast milk samples and 2171 environmental swabs were collected. Sociodemographic, clinical, cultural and biological data were collected at enrolment and at each follow-up visit using Research Electronic Data Capture.

FINDINGS TO DATE: Baseline characteristics of 98/107 mother-infant dyads are included in the analysis. The cohort reflects an urban low-income population: median household income was PKR 30,000 per month (approximately US$170 per capita per month). Caesarean section accounted for 55% (54/98) of deliveries; 13.0% of infants were late preterm, and 10.0% had low birth weight (<2500 g). Breastfeeding was the predominant feeding mode though only 24 infants were exclusively breastfed from birth to 6 months. Antibiotics were prescribed to almost all mothers following delivery, and 19 infants received antibiotics during follow-up, most commonly amikacin combined with ceftazidime.

FUTURE PLAN: Shotgun metagenomic sequencing of infant stool samples is underway to enable species-level and plasmid-level profiling of microbial communities and ARGs. Subject to funding, hybrid long- and short-read sequencing and extended follow-up to 24 months are planned.},
}

Humans
Pakistan
Female
Infant
Longitudinal Studies
Infant, Newborn
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Male
Breast Feeding/statistics & numerical data
Anti-Bacterial Agents/therapeutic use
Birth Cohort
Adult
Milk, Human/microbiology

@article {pmid42761040,
year = {2026},
author = {Ribeiro, GO and Guimarães, LO and Foro Ramos, EDS and Couto, RDS and Telles-de-Deus, J and Helfstein, VC and Morais, VDS and Reginato, SL and Mucci, LF and Bergo, ES and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Leal, É and Kirchgatter, K},
title = {RNA virome comparison between sylvatic and urban-interface mosquitoes from Southeastern Brazil.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1894867},
pmid = {42761040},
issn = {2235-2988},
mesh = {Animals ; Brazil ; *Virome/genetics ; *Culicidae/virology/classification ; *RNA, Viral/genetics ; *Mosquito Vectors/virology ; *RNA Viruses/genetics/classification/isolation & purification ; Forests ; },
abstract = {INTRODUCTION: Mosquitoes (Diptera: Culicidae) are primary vectors of public health pathogens, yet their core viromes remain poorly characterized, particularly in Neotropical sylvatic lineages. This study investigated the RNA virome of multiple mosquito species across urban-to-forest gradients in São Paulo State, Brazil, including neglected sylvatic taxa such as Sabethes, Psorophora, Shannoniana, and Wyeomyia.

METHODS: The RNA virome of multiple mosquito species was investigated across urban-to-forest gradients in São Paulo State, Brazil. Ecological analyses were performed to assess the effects of host taxonomy and environment on virome composition. Network analysis was conducted to investigate virus-host associations and viral sharing across ecological interfaces.

RESULTS: Our analysis identified 919 viral contigs across 217 viral species and 37 distinct families, revealing a substantial fraction of "viral dark matter" with low amino acid identity (median < 40%) in predominantly sylvatic mosquito species. Although viral families containing known arboviruses, such as Flaviviridae, Phenuiviridae, and Peribunyaviridae, were detected, no high-consequence human pathogens were identified within the sensitivity limits of our sampling and sequencing depth. Ecological analyses demonstrated that virome composition was strongly structured by host taxonomy and environment (R[2]=0.570, p=0.001), with host species explaining 32.9% of the unique variance (PERMANOVA, R[2]=0.329, p=0.001), whereas ecotope played a secondary role (R[2]=0.029, p=0.001). Network analysis revealed a highly modular virus-host structure dominated by host-restricted specialists, with a limited number of bridge species facilitating viral sharing across ecological interfaces.

DISCUSSION: These findings indicate that intrinsic mosquito biology is the main driver of viral community structure, while environmental gradients play a secondary role, and highlight the importance of host-associated processes in shaping viral diversity at the Neotropical forest-urban interface.},
}

Animals
Brazil
*Virome/genetics
*Culicidae/virology/classification
*RNA, Viral/genetics
*Mosquito Vectors/virology
*RNA Viruses/genetics/classification/isolation & purification
Forests

@article {pmid41667306,
year = {2026},
author = {Tong, Y and Chen, Y and Dong, Y and Chen, K and Yang, J and Dong, X and Wan, X and Luo, Z and Fang, J and Liu, Y and Li, W and Wang, Z and Gu, X},
title = {Characterization of the oral microbiota of Kawasaki disease patients by metagenomic analysis: A pilot study.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {59},
number = {5},
pages = {556-564},
doi = {10.1016/j.jmii.2026.01.007},
pmid = {41667306},
issn = {1995-9133},
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/drug therapy ; Female ; Male ; *Metagenomics/methods ; Pilot Projects ; Child, Preschool ; *Microbiota/genetics ; *Mouth/microbiology ; Immunoglobulins, Intravenous/therapeutic use ; Infant ; Bacteria/classification/genetics/isolation & purification ; Child ; Metagenome ; },
abstract = {BACKGROUND: Kawasaki disease (KD) is an acute febrile systemic vasculitis characterized by vascular inflammation. Its pathogenesis has been linked to the infiltration of IgA[+] plasma cells within the respiratory tract, suggesting the upper airway may act as a potential portal of entry. However, evidence connecting respiratory infections to KD remains limited. This study aimed to explore the relationship between oral microbiota and KD development.

METHODS: Oral swab samples were collected from 25 KD patients before and after intravenous immunoglobulin (IVIG) treatment, as well as from 25 healthy controls. Metagenomic sequencing was performed to characterize overall microbial composition and identify potential microbial markers associated with KD.

RESULTS: Significant alterations in oral microbiota composition were observed between KD patients and healthy controls. The diversity of oral microbiota in KD patients was markedly lower than that in healthy controls, and exhibited an upward trend following IVIG treatment. Elevated levels of Streptococcus, Prevotella, and Veillonella, along with reduced levels of Haemophilus, Neisseria, and Rothia, were closely associated with KD development. Putative novel pathogen Abiotrophia defectiva was significantly enriched in patients with KD. Correlation analysis revealed that the relative abundances of several Haemophilus species were positively correlated with albumin levels in KD patients before IVIG treatment. Additionally, the anti-inflammatory bacterium Rothia mucilaginosa may play a protective role against the development of coronary artery lesions in KD.

CONCLUSION: These findings provide new evidence that distinct alterations in the oral microbiome are associated with KD development. Oral microbiota-based biomarkers may represent a potential strategy for KD therapy.},
}

Humans
*Mucocutaneous Lymph Node Syndrome/microbiology/drug therapy
Female
Male
*Metagenomics/methods
Pilot Projects
Child, Preschool
*Microbiota/genetics
*Mouth/microbiology
Immunoglobulins, Intravenous/therapeutic use
Infant
Bacteria/classification/genetics/isolation & purification
Child
Metagenome

@article {pmid42259841,
year = {2026},
author = {Deng, F and Fan, Y and Yan, J and Zhang, X and Guo, Y and Li, M and Peng, Y and Zhao, L and Liu, F and Zheng, Y and Deng, B and Deng, J and Chen, S and Jiang, H and Chai, J and Zhao, J and Li, Y},
title = {Genome-resolved and culture-based atlas of the feline gut microbiome enables host-adapted probiotic development.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42259841},
issn = {2055-5008},
mesh = {Animals ; Cats/microbiology ; *Probiotics ; Feces/microbiology ; Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; Genome, Bacterial ; Escherichia coli ; },
abstract = {Domestic cats (Felis catus) depend on their gut microbiome for metabolism, immunity, and pathogen defense, yet its genomic characterization remains limited. We combined large-scale metagenomics and culturomics to define the feline gut microbiome and identify indigenous probiotic candidates. Analysis of 412 feline fecal metagenomes produced 2852 strain-resolved metagenome-assembled genomes (MAGs) grouped into 514 species-level genome bins, including 106 putative novel taxa. This catalog revealed 24 core species and two enterotypes: ET-P, deaminated by Prevotella, and ET-CB, enriched for Collinsella, Blautia, Bifidobacterium, Ligilactobacillus, MAG-based screening prioritized 113 candidate probiotic species. Culturomics recovered 2904 isolates representing 110 species-level taxa, including 75 putative novel species and a candidate novel genus. Six feline-derived isolates were selected for downstream testing, and five exhibited favorable probiotic traits in vitro, including acid and bile tolerance, anti-Escherichia coli activity, and favorable cytokine responses. In a pathogenic Escherichia coli-induced dirrhea model in cats, a five-strain indigenous consortium improved fecal scores and reduced IL-2, IL-1β, and IL-6, with TNF-α suppression superior to antibiotics or a commercial probiotic. These results establish FelMGDB as a resource for feline microbiome research and highlights indigenous probiotics as promising interventions for feline gut health.},
}

Animals
Cats/microbiology
*Probiotics
Feces/microbiology
Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Metagenome
*Bacteria/classification/genetics/isolation & purification
Phylogeny
Genome, Bacterial
Escherichia coli